From 42d5ae9a4790f9515b7923c299374171ac3cb093 Mon Sep 17 00:00:00 2001 From: RamonaWalls Date: Wed, 12 Feb 2020 19:32:00 -0700 Subject: [PATCH] add files for release --- imports/bfo_import.obo | 260 + imports/bfo_import.owl | 676 +- imports/envo_import.obo | 72 + imports/envo_import.owl | 2189 +-- imports/go_import.obo | 119 + imports/go_import.owl | 179 +- imports/ncbitaxon_import.obo | 330 + imports/ncbitaxon_import.owl | 12 +- imports/pato_import.obo | 97 + imports/pato_import.owl | 252 +- imports/ro_import.obo | 1321 ++ imports/ro_import.owl | 1849 +- pco-base.obo | 493 + pco-base.owl | 1244 ++ pco-full.obo | 1820 ++ pco-full.owl | 4991 ++++++ pco.obo | 1820 ++ pco.owl | 14276 ++-------------- reports/pco-edit.owl-obo-report.tsv | 24 + src/ontology/Makefile | 12 +- src/ontology/imports/envo_import.obo | 71 + src/ontology/imports/go_import.obo | 118 + src/ontology/imports/ncbitaxon_import.obo | 550 + src/ontology/imports/pato_import.obo | 96 + src/ontology/pco-base.obo | 493 + src/ontology/pco-base.owl | 1244 ++ src/ontology/pco-edit.owl | 3 +- src/ontology/pco-full.obo | 1820 ++ src/ontology/pco-full.owl | 4991 ++++++ src/ontology/pco.obo | 1820 ++ src/ontology/pco.owl | 14270 ++------------- .../reports/pco-edit.owl-obo-report.tsv | 24 + 32 files changed, 30099 insertions(+), 27437 deletions(-) create mode 100644 imports/bfo_import.obo create mode 100644 imports/envo_import.obo create mode 100644 imports/go_import.obo create mode 100644 imports/ncbitaxon_import.obo create mode 100644 imports/pato_import.obo create mode 100644 imports/ro_import.obo create mode 100644 pco-base.obo create mode 100644 pco-base.owl create mode 100644 pco-full.obo create mode 100644 pco-full.owl create mode 100644 pco.obo create mode 100644 reports/pco-edit.owl-obo-report.tsv create mode 100644 src/ontology/imports/envo_import.obo create mode 100644 src/ontology/imports/go_import.obo create mode 100644 src/ontology/imports/ncbitaxon_import.obo create mode 100644 src/ontology/imports/pato_import.obo create mode 100644 src/ontology/pco-base.obo create mode 100644 src/ontology/pco-base.owl create mode 100644 src/ontology/pco-full.obo create mode 100644 src/ontology/pco-full.owl create mode 100644 src/ontology/pco.obo create mode 100644 src/ontology/reports/pco-edit.owl-obo-report.tsv diff --git a/imports/bfo_import.obo b/imports/bfo_import.obo new file mode 100644 index 0000000..3a3dcb0 --- /dev/null +++ b/imports/bfo_import.obo @@ -0,0 +1,260 @@ +format-version: 1.2 +data-version: pco/imports/bfo_import/pco/releases/2020-02-13/bfo_import.owl/pco/imports/bfo_import.obo +ontology: pco/imports/bfo_import.obo + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf", comment="per discussion with Barry Smith"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: BFO:0000179 "continuant" xsd:string +property_value: BFO:0000180 "Continuant" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: BFO:0000179 "occurrent" xsd:string +property_value: BFO:0000180 "Occurrent" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "ic" xsd:string +property_value: BFO:0000180 "IndependentContinuant" xsd:string +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +is_a: BFO:0000003 ! occurrent +property_value: BFO:0000179 "process" xsd:string +property_value: BFO:0000180 "Process" xsd:string +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +is_a: BFO:0000020 ! specifically dependent continuant +property_value: BFO:0000179 "realizable" xsd:string +property_value: BFO:0000180 "RealizableEntity" xsd:string +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "sdc" xsd:string +property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +is_a: BFO:0000017 ! realizable entity +property_value: BFO:0000179 "role" xsd:string +property_value: BFO:0000180 "Role" xsd:string +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000027 +name: object aggregate +is_a: BFO:0000040 ! material entity +property_value: BFO:0000179 "object-aggregate" xsd:string +property_value: BFO:0000180 "ObjectAggregate" xsd:string +property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string +property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string +property_value: IAO:0000112 "a symphony orchestra" xsd:string +property_value: IAO:0000112 "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)" xsd:string +property_value: IAO:0000112 "defined by fiat: the aggregate of members of an organization" xsd:string +property_value: IAO:0000112 "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string +property_value: IAO:0000112 "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string +property_value: IAO:0000112 "defined via attributive delimitations such as: the patients in this hospital" xsd:string +property_value: IAO:0000112 "the aggregate of bearings in a constant velocity axle joint" xsd:string +property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:string +property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string +property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string +property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string +property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} +property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000029 +name: site +is_a: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "site" xsd:string +property_value: BFO:0000180 "Site" xsd:string +property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string +property_value: IAO:0000112 "a rabbit hole" xsd:string +property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string +property_value: IAO:0000112 "Manhattan Canyon)" xsd:string +property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string +property_value: IAO:0000112 "the Grand Canyon" xsd:string +property_value: IAO:0000112 "the hold of a ship" xsd:string +property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string +property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string +property_value: IAO:0000112 "the interior of your bedroom" xsd:string +property_value: IAO:0000112 "the interior of your office" xsd:string +property_value: IAO:0000112 "the interior of your refrigerator" xsd:string +property_value: IAO:0000112 "the lumen of your gut" xsd:string +property_value: IAO:0000112 "the Piazza San Marco" xsd:string +property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string +property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +is_a: BFO:0000002 ! continuant +property_value: BFO:0000179 "gdc" xsd:string +property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "material" xsd:string +property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant +property_value: BFO:0000179 "immaterial" xsd:string +property_value: BFO:0000180 "ImmaterialEntity" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + diff --git a/imports/bfo_import.owl b/imports/bfo_import.owl index baec420..d0e3934 100644 --- a/imports/bfo_import.owl +++ b/imports/bfo_import.owl @@ -1,13 +1,15 @@ - + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> + + + @@ -22,15 +24,134 @@ + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -48,8 +169,32 @@ + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + entity + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + @@ -57,8 +202,140 @@ + + continuant + Continuant + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + continuant + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + + + + + occurrent + Occurrent + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + @@ -66,7 +343,27 @@ + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + independent continuant @@ -75,6 +372,195 @@ b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + @@ -82,8 +568,59 @@ + object-aggregate + ObjectAggregate + a collection of cells in a blood biobank. + a swarm of bees is an aggregate of members who are linked together through natural bonds + a symphony orchestra + an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) + defined by fiat: the aggregate of members of an organization + defined through physical attachment: the aggregate of atoms in a lump of granite + defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container + defined via attributive delimitations such as: the patients in this hospital + the aggregate of bearings in a constant velocity axle joint + the aggregate of blood cells in your body + the nitrogen atoms in the atmosphere + the restaurants in Palo Alto + your collection of Meissen ceramic plates. + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + object aggregate + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + + + + + + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + + + + + + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + @@ -91,8 +628,69 @@ + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + site + + + + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + + + + + + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + @@ -101,8 +699,68 @@ + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + material entity + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + @@ -110,11 +768,15 @@ + immaterial + ImmaterialEntity + BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 + immaterial entity - + diff --git a/imports/envo_import.obo b/imports/envo_import.obo new file mode 100644 index 0000000..afdec1c --- /dev/null +++ b/imports/envo_import.obo @@ -0,0 +1,72 @@ +format-version: 1.2 +data-version: pco/imports/envo_import/pco/releases/2020-02-13/envo_import.owl/pco/imports/envo_import.obo +default-namespace: ENVO +remark: ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. \n\nNew terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ \n\n\nPlease see www.environmentontology.org for more information and citations. +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 186 Logical Axioms: 30] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 114 Logical Axioms: 19] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 132 Logical Axioms: 23] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 40 Logical Axioms: 6] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 21 Logical Axioms: 2] +ontology: pco/imports/envo_import.obo +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-6601-2165 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8343-612X xsd:string +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0003-1604-1512 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0002-6962-2807 xsd:string + +[Term] +id: ENVO:00000070 +name: construction +def: "A feature that has been constructed by deliberate human effort." [MA:ma] +synonym: "constructed feature" EXACT [] +is_a: BFO:0000040 +is_a: ENVO:00002297 ! environmental feature +is_a: ENVO:01000813 ! astronomical body part +property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string + +[Term] +id: ENVO:00002297 +name: environmental feature +def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] +comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. +is_a: BFO:0000040 + +[Term] +id: ENVO:01000254 +name: environmental system +def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +synonym: "environment" EXACT [] +xref: EcoLexicon:environment +is_a: BFO:0000040 +creation_date: 2013-09-23T16:04:08Z + +[Term] +id: ENVO:01000744 +name: human dwelling +def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] +is_a: ENVO:00000070 ! construction +property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string + +[Term] +id: ENVO:01000813 +name: astronomical body part +def: "A material part of an astronomical body." [] +subset: envoAstro +subset: envoPolar +is_a: BFO:0000040 +is_a: ENVO:00002297 ! environmental feature + +[Term] +id: ENVO:01001369 +name: tidal mangrove shrubland +alt_id: CMECS:577 +def: "A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas." [] +comment: This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" +subset: envoCmecs +subset: envoMarine +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ENVO:01000254 ! environmental system +created_by: http://orcid.org/0000-0002-4366-3088 + diff --git a/imports/envo_import.owl b/imports/envo_import.owl index 0f48b7b..69bb002 100644 --- a/imports/envo_import.owl +++ b/imports/envo_import.owl @@ -1,92 +1,41 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + http://orcid.org/0000-0002-4366-3088 + http://orcid.org/0000-0002-6601-2165 + http://orcid.org/0000-0002-8343-612X + http://orcid.org/0000-0003-1604-1512 + https://orcid.org/0000-0002-6962-2807 + ENVO + ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. - +New terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +Please see www.environmentontology.org for more information and citations. + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 186 Logical Axioms: 30] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 114 Logical Axioms: 19] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 132 Logical Axioms: 23] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>) VersionIRI(<null>))) [Axioms: 40 Logical Axioms: 6] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>) VersionIRI(<null>))) [Axioms: 21 Logical Axioms: 2] + @@ -94,453 +43,107 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - + + definition + - + - - - - + + editor note + - + - - - - + - + - - - - - + - + - + - + - - - - - + - + - - - - - - - - + + has_alternative_id + - + - - - + - + - - - - - - - - - - - - - - - - - - true - + + has_exact_synonym + - + - - - - + + has_obo_namespace + - + - - - + + has_related_synonym + - + - - - - - - - - + - + - - - - - + + in_subset + - + - - - + - + - + @@ -555,1638 +158,120 @@ - - - - entity - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - continuant - - - - - + - - - An entity that has temporal parts and that happens, unfolds or develops through time. - occurrent - + - + - - - - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - independent continuant + + + + + A feature that has been constructed by deliberate human effort. + "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference + constructed feature + construction - + - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - + A feature that has been constructed by deliberate human effort. + MA:ma - + - - - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - process + + + A material entity which determines an environmental system. + ENVO + ENVO:00002297 + A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. + environmental feature - + - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - + A material entity which determines an environmental system. + DOI:10.1186/2041-1480-4-43 + NM:nm + ORCID:0000-0002-4366-3088 - - - - - quality - - - - - + - - - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - specifically dependent continuant + + + A system which has the disposition to environ one or more material entities. + 2013-09-23T16:04:08Z + EcoLexicon:environment + environment + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system - + - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - + A system which has the disposition to environ one or more material entities. + DOI:10.1186/2041-1480-4-43 - - - - - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - generically dependent continuant - - - - - - - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity - - - - - + - - - anatomical structure + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. + Subclasses will be added by inference. + human dwelling + + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 + - + - + - material anatomical entity + + A material part of an astronomical body. + envoAstro + envoPolar + astronomical body part - + - - - macroscopic spatial feature - geographic feature + + + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. + http://orcid.org/0000-0002-4366-3088 + CMECS:577 + https://cmecscatalog.org/cmecs/classification/unit/577.html + envoCmecs + envoMarine + This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" + tidal mangrove shrubland - - - - - - - - An anthropogenic geographic feature is a geographic feature -resulting from the influence of human beings on nature. - man-made feature - manmade feature - anthropogenic geographic feature - - - - - An anthropogenic geographic feature is a geographic feature -resulting from the influence of human beings on nature. - ORCID:0000-0002-4366-3088 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A feature that has been constructed by deliberate human effort. - constructed feature - construction - - - - - A feature that has been constructed by deliberate human effort. - MA:ma - - - - - - - - - An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff. - mesoscopic physical object - - - - - An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff. - MA:ma - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity which determines an environmental system. - environmental feature - - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. - manufactured good - manufactured product - - - - - A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. - https://en.wikipedia.org/wiki/Manufactured_product - - - - - - - - - anthropogenic abiotic mesoscopic feature - - - - - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - portion of environmental material - environmental material - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - DOI:10.1186/2041-1480-4-43 - MA:ma - ORCID:0000-0002-4366-3088 - URL:http://ontology.buffalo.edu/smith/articles/niches.html - - - - - - - - - abiotic mesoscopic physical object - - - - - - - - - A system which has the disposition to environ one or more material entities. - environment - environmental system - - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anthropogenic environment is an environmental system which is the product of human activity. - anthropogenic environment - - - - - - - - - Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. - space - outer space - - - - - Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. - https://en.wikipedia.org/wiki/Outer_space - - - - - - - - - A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. - human dwelling - - - - - A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. - https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 - - - - - - - - - An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. - celestial body - astronomical body - - - - - An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. - https://en.wikipedia.org/wiki/Astronomical_object - - - - - - - - - - - - - - - - - - 1 - - - - An object which is composed of one or more gravitationally bound structures that are associated with a position in space. - celestial object - astronomical object - - - - - An object which is composed of one or more gravitationally bound structures that are associated with a position in space. - https://en.wikipedia.org/wiki/Astronomical_object - - - - - - - - - - - - - - - A material part of an astronomical body. - astronomical body part - - - - - - - - - - - - - - - - A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with. - biosphere - - - - - A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with. - http://www.biology-online.org/dictionary/Biosphere - https://en.wikipedia.org/wiki/Biosphere - - - - - - - - - - - - - - - - - - - - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - natural environment - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - https://en.wikipedia.org/wiki/Anthropization - https://en.wikipedia.org/wiki/Natural_environment - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process during which a natural environmental system is altered by human action. - anthropization - anthropisation - - - - - A process during which a natural environmental system is altered by human action. - https://en.wikipedia.org/wiki/Anthropization - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body. - technosphere - - - - - An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body. - http://dx.doi.org/10.1177/2053019616677743 - http://www.yourdictionary.com/technosphere - https://www.sciencedaily.com/releases/2016/11/161130085021.htm - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. - manufacturing process - - - - - A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. - https://en.wikipedia.org/wiki/Manufacturing - - - - - - - - - - - - - - - - - - - - - - - - - - An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures. - construction process - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by materials bearing roughly homogeneous qualities. - environmental system determined by a quality - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system within which an environmental material strongly influences the system's composition and properties. - environmental system determined by a material - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by a living organism. - host-associated environment - environmental system determined by an organism - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by an animal. - animal environment - Metazoan-associated environment - animal-associated environment - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead animal, or a whole small animal. - environment associated with an animal part or small animal - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead plant, or a whole small plant. - environment associated with a plant part or small plant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which includes both living and non-living components. - ecosystem - - - - - An environmental system which includes both living and non-living components. - https://en.wikipedia.org/wiki/Ecosystem - - - - - - - - - - - - - - - - - - - - - - - A process in which includes the components of an environmental system as participants. - environmental system process - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental process which is driven by the action of humans. - anthropogenic environmental process - - - - - - - - - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - biological process - physiological process - biological_process - - - - - - - - - all - root - - - - - all - - - - - - - - - - Teleostomi - - - - - - - - - bony vertebrates - Euteleostomi - - - - - - - - - biota - cellular organisms - - - - - biota - - - - - - - - - - Dipnotetrapodomorpha - - - - - - - - - Boreotheria - Boreoeutheria - - - - - - - - - Homo/Pan/Gorilla group - Homininae - - - - - - - - - eucaryotes - eukaryotes - Eucarya - Eucaryotae - Eukarya - Eukaryotae - eukaryotes - Eukaryota - - - - - eucaryotes - - - - - - eukaryotes - - - - - - Eucarya - - - - - - Eucaryotae - - - - - - Eukarya - - - - - - Eukaryotae - - - - - - eukaryotes - - - - - - - - - - Euarchontoglires - - - - - - - - - Anthropoidea - Simiiformes - - - - - - - - - ape - apes - Hominoidea - - - - - - - - - tetrapods - Tetrapoda - - - - - - - - - amniotes - Amniota - - - - - - - - - Theria - Theria <Mammalia> - - - - - - - - - Fungi/Metazoa group - opisthokonts - Opisthokonta - - - - - - - - - metazoans - multicellular animals - Animalia - animals - Metazoa - - - - - - - - - Bilateria - - - - - - - - - deuterostomes - Deuterostomia - - - - - - - - - Haplorrhini - - - - - - - - - mammals - mammals - Mammalia - - - - - - - - - Eumetazoa - - - - - - - - - chordates - chordates - Chordata - - - - - - - - - Vertebrata - vertebrates - vertebrates - Vertebrata <Metazoa> - - - - - - - - - Gnathostomata - jawed vertebrates - Gnathostomata <vertebrate> - - - - - - - - - Sarcopterygii - - - - - - - - - Craniata - Craniata <chordata> - - - - - - - - - eutherian mammals - placental mammals - placentals - Placentalia - placentals - Eutheria - - - - - - - - - primate - Primata - primates - Primates - - - - - - - - - Catarrhini - - - - - - - - - great apes - Pongidae - Hominidae - - - - - - - - - Homo - - - - - - - - - human - man - humans - Homo sapiens - - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - trait - quality - - - - - - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - morphology - - - - - - - - - qualitative - - - - - - - - - A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. - deviation(from_normal) - - - - - - - - - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. - size - - - - - - - - - - A size quality which is relatively low. - hypoplasia - underdeveloped - reduced - small - tiny - decreased size - - - - - - - - - A quality which inheres in a continuant. - monadic quality of a continuant - multiply inhering quality of a physical entity - quality of a continuant - quality of a single physical entity - quality of an object - quality of continuant - monadic quality of an object - monadic quality of continuant - physical object quality - - - - - - - - - A quality that has a value that is decreased compared to normal or average. - decreased quality - - - - - - - - - - A quality of an object that has a value that is decreased compared to normal or average. - decreased object quality - - - - - - - - A material entity that consists of two or more organisms, viruses, or viroids. - collection of organisms - - - - - - - - - A plant structure (PO:0005679) which is a whole organism. - genet (broad) - ramet (broad) - planta entera (Spanish, exact) - 植物体全体 (Japanese, exact) - bush (narrow) - frutex (narrow) - frutices (narrow) - gametophyte (narrow) - herb (narrow) - liana (narrow) - prothalli (narrow) - prothallium (narrow) - prothallus (narrow) - seedling (narrow) - shrub (narrow) - sporophyte (narrow) - suffrutex (narrow) - suffrutices (narrow) - tree (narrow) - vine (narrow) - woody clump (narrow) - clonal colony (related) - colony (related) - whole plant - - - - - - - - - An anatomical structure that is or was part of a plant, or was derived from a part of a plant. - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) - plant structure - - - - - - - - - An anatomical entity that is or was part of a plant. - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) - plant anatomical entity - - - - - - - - - A material entity consisting of multiple components that are causally integrated. - system - - - - - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - anatomical entity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff --git a/imports/go_import.obo b/imports/go_import.obo new file mode 100644 index 0000000..b44e307 --- /dev/null +++ b/imports/go_import.obo @@ -0,0 +1,119 @@ +format-version: 1.2 +data-version: pco/releases/2020-02-13/go_import.obo +ontology: pco/imports/go_import.obo + +[Term] +id: GO:0007610 +name: behavior +namespace: biological_process +alt_id: GO:0044708 +def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] +comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). +subset: gocheck_do_not_manually_annotate +subset: goslim_agr +subset: goslim_flybase_ribbon +synonym: "behavioral response to stimulus" EXACT [] +synonym: "behaviour" EXACT [] +synonym: "behavioural response to stimulus" EXACT [] +synonym: "single-organism behavior" RELATED [] +xref: Wikipedia:Behavior +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-20T14:06:08Z + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0035176 +name: social behavior +namespace: biological_process +def: "Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group." [GOC:jh2, PMID:12848939, Wikipedia:Social_behavior] +comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. +synonym: "cooperative behavior" RELATED [] +synonym: "social behaviour" EXACT [] +xref: Wikipedia:Social_behavior +is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051705 ! multi-organism behavior +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0044419 +name: interspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +subset: goslim_candida +subset: goslim_pir +synonym: "interaction with another species" EXACT [] +synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051703 +name: intraspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: goslim_pir +synonym: "intraspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051704 +name: multi-organism process +namespace: biological_process +alt_id: GO:0051706 +def: "A biological process which involves another organism of the same or different species." [GOC:jl] +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "interaction between organisms" EXACT [] +synonym: "physiological interaction between organisms" EXACT [] +synonym: "physiological interaction with other organism" EXACT [] +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051705 +name: multi-organism behavior +namespace: biological_process +alt_id: GO:0023032 +alt_id: GO:0044709 +def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] +subset: goslim_pir +synonym: "behavioral interaction between organisms" EXACT [] +synonym: "behavioral interaction with other organism" EXACT [] +synonym: "behavioral signaling" NARROW [] +synonym: "behavioral signalling" NARROW [GOC:mah] +synonym: "behavioural interaction between organisms" EXACT [] +synonym: "behavioural interaction with other organism" EXACT [] +is_a: GO:0007610 ! behavior +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + diff --git a/imports/go_import.owl b/imports/go_import.owl index b95c935..3644886 100644 --- a/imports/go_import.owl +++ b/imports/go_import.owl @@ -1,14 +1,16 @@ - + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + @@ -25,31 +27,124 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + - + + + - + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -69,10 +164,22 @@ The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + janelomax + 2012-09-20T14:06:08Z + GO:0044708 + Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus + biological_process single-organism behavior + GO:0007610 + + + + 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. +2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). + behavior @@ -90,19 +197,37 @@ - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + janelomax + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process biological process physiological process + biological_process single organism process single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + biological_process - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - GOC:go_curators - GOC:isa_complete + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt @@ -113,8 +238,13 @@ Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + Wikipedia:Social_behavior social behaviour + biological_process cooperative behavior + GO:0035176 + Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. + social behavior @@ -136,6 +266,11 @@ interaction with another species interspecies interaction interspecies interaction with other organisms + biological_process + GO:0044419 + + + interspecies interaction between organisms @@ -153,6 +288,10 @@ Any process in which an organism has an effect on an organism of the same species. intraspecies interaction with other organisms + biological_process + GO:0051703 + + intraspecies interaction between organisms @@ -169,9 +308,15 @@ A biological process which involves another organism of the same or different species. + GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism + biological_process + GO:0051704 + + + multi-organism process @@ -189,12 +334,18 @@ Any process in which an organism has a behavioral effect on another organism of the same or different species. + GO:0023032 + GO:0044709 behavioral interaction between organisms behavioral interaction with other organism behavioural interaction between organisms behavioural interaction with other organism behavioral signaling behavioral signalling + biological_process + GO:0051705 + + multi-organism behavior @@ -213,5 +364,5 @@ - + diff --git a/imports/ncbitaxon_import.obo b/imports/ncbitaxon_import.obo new file mode 100644 index 0000000..39455ea --- /dev/null +++ b/imports/ncbitaxon_import.obo @@ -0,0 +1,330 @@ +format-version: 1.2 +data-version: pco/releases/2020-02-13/ncbitaxon_import.obo +ontology: pco/imports/ncbitaxon_import.obo + +[Term] +id: NCBITaxon:1 +name: root +synonym: "all" RELATED synonym [] + +[Term] +id: NCBITaxon:10239 +name: Viruses +synonym: "Vira" RELATED synonym [] +synonym: "Viridae" RELATED synonym [] +synonym: "viruses" RELATED blast_name [] +is_a: NCBITaxon:1 ! root + +[Term] +id: NCBITaxon:117570 +name: Teleostomi +is_a: NCBITaxon:7776 ! Gnathostomata + +[Term] +id: NCBITaxon:117571 +name: Euteleostomi +synonym: "bony vertebrates" EXACT genbank_common_name [] +is_a: NCBITaxon:117570 ! Teleostomi + +[Term] +id: NCBITaxon:12884 +name: Viroids +synonym: "Viroid" RELATED synonym [] +synonym: "viroids" RELATED blast_name [] +is_a: NCBITaxon:1 ! root + +[Term] +id: NCBITaxon:131221 +name: Streptophytina +synonym: "Charophyta/Embryophyta group" RELATED synonym [] +synonym: "charophyte/embryophyte group" RELATED synonym [] +is_a: NCBITaxon:35493 ! Streptophyta + +[Term] +id: NCBITaxon:131567 +name: cellular organisms +synonym: "biota" RELATED synonym [] +is_a: NCBITaxon:1 ! root + +[Term] +id: NCBITaxon:1338369 +name: Dipnotetrapodomorpha +is_a: NCBITaxon:8287 ! Sarcopterygii + +[Term] +id: NCBITaxon:1437010 +name: Boreoeutheria +synonym: "Boreotheria" RELATED synonym [] +is_a: NCBITaxon:9347 ! Eutheria + +[Term] +id: NCBITaxon:1437180 +name: Acrogymnospermae +is_a: NCBITaxon:58024 ! Spermatophyta + +[Term] +id: NCBITaxon:2 +name: Bacteria +synonym: "bacteria" RELATED blast_name [] +synonym: "eubacteria" EXACT genbank_common_name [] +synonym: "Monera" RELATED in_part [] +synonym: "not Bacteria Haeckel 1894" RELATED synonym [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +is_a: NCBITaxon:131567 ! cellular organisms + +[Term] +id: NCBITaxon:207598 +name: Homininae +synonym: "Homo/Pan/Gorilla group" RELATED synonym [] +is_a: NCBITaxon:9604 ! Hominidae + +[Term] +id: NCBITaxon:2157 +name: Archaea +synonym: "archaea" RELATED blast_name [] +synonym: "Archaebacteria" RELATED synonym [] +synonym: "Mendosicutes" RELATED synonym [] +synonym: "Metabacteria" RELATED synonym [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +is_a: NCBITaxon:131567 ! cellular organisms + +[Term] +id: NCBITaxon:2759 +name: Eukaryota +synonym: "Eucarya" RELATED synonym [] +synonym: "Eucaryotae" RELATED synonym [] +synonym: "eucaryotes" EXACT genbank_common_name [] +synonym: "Eukarya" RELATED synonym [] +synonym: "Eukaryotae" RELATED synonym [] +synonym: "eukaryotes" EXACT common_name [] +synonym: "eukaryotes" RELATED blast_name [] +is_a: NCBITaxon:131567 ! cellular organisms + +[Term] +id: NCBITaxon:3041 +name: Chlorophyta +synonym: "algae" RELATED in_part [] +synonym: "Chlorophycota" RELATED synonym [] +synonym: "Chlorophyta sensu Bremer 1985" RELATED synonym [] +synonym: "green algae" EXACT genbank_common_name [] +synonym: "green algae" RELATED blast_name [] +is_a: NCBITaxon:33090 ! Viridiplantae + +[Term] +id: NCBITaxon:314146 +name: Euarchontoglires +is_a: NCBITaxon:1437010 ! Boreoeutheria + +[Term] +id: NCBITaxon:314293 +name: Simiiformes +synonym: "Anthropoidea" RELATED synonym [] +is_a: NCBITaxon:376913 ! Haplorrhini + +[Term] +id: NCBITaxon:314295 +name: Hominoidea +synonym: "ape" EXACT common_name [] +synonym: "apes" EXACT genbank_common_name [] +is_a: NCBITaxon:9526 ! Catarrhini + +[Term] +id: NCBITaxon:3193 +name: Embryophyta +synonym: "higher plants" EXACT common_name [] +synonym: "land plants" EXACT common_name [] +synonym: "land plants" RELATED blast_name [] +synonym: "plants" EXACT common_name [] +is_a: NCBITaxon:131221 ! Streptophytina + +[Term] +id: NCBITaxon:32523 +name: Tetrapoda +synonym: "tetrapods" EXACT genbank_common_name [] +is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha + +[Term] +id: NCBITaxon:32524 +name: Amniota +synonym: "amniotes" EXACT genbank_common_name [] +is_a: NCBITaxon:32523 ! Tetrapoda + +[Term] +id: NCBITaxon:32525 +name: Theria +synonym: "Theria" EXACT scientific_name [] +is_a: NCBITaxon:40674 ! Mammalia + +[Term] +id: NCBITaxon:33090 +name: Viridiplantae +synonym: "Chlorobionta" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] +synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "green plants" EXACT common_name [] +synonym: "green plants" RELATED blast_name [] +is_a: NCBITaxon:2759 ! Eukaryota + +[Term] +id: NCBITaxon:33154 +name: Opisthokonta +synonym: "Fungi/Metazoa group" RELATED synonym [] +synonym: "opisthokonts" RELATED synonym [] +is_a: NCBITaxon:2759 ! Eukaryota + +[Term] +id: NCBITaxon:33208 +name: Metazoa +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT common_name [] +is_a: NCBITaxon:33154 ! Opisthokonta + +[Term] +id: NCBITaxon:33213 +name: Bilateria +is_a: NCBITaxon:6072 ! Eumetazoa + +[Term] +id: NCBITaxon:33511 +name: Deuterostomia +synonym: "deuterostomes" EXACT common_name [] +is_a: NCBITaxon:33213 ! Bilateria + +[Term] +id: NCBITaxon:3398 +name: Magnoliophyta +synonym: "Angiospermae" RELATED synonym [] +synonym: "angiosperms" EXACT common_name [] +synonym: "flowering plants" EXACT genbank_common_name [] +synonym: "flowering plants" RELATED blast_name [] +is_a: NCBITaxon:58024 ! Spermatophyta + +[Term] +id: NCBITaxon:35493 +name: Streptophyta +is_a: NCBITaxon:33090 ! Viridiplantae + +[Term] +id: NCBITaxon:376913 +name: Haplorrhini +is_a: NCBITaxon:9443 ! Primates + +[Term] +id: NCBITaxon:40674 +name: Mammalia +synonym: "mammals" EXACT genbank_common_name [] +synonym: "mammals" RELATED blast_name [] +is_a: NCBITaxon:32524 ! Amniota + +[Term] +id: NCBITaxon:58023 +name: Tracheophyta +synonym: "vascular plants" EXACT common_name [] +synonym: "vascular plants" RELATED blast_name [] +is_a: NCBITaxon:3193 ! Embryophyta + +[Term] +id: NCBITaxon:58024 +name: Spermatophyta +synonym: "seed plants" EXACT common_name [] +synonym: "seed plants" RELATED blast_name [] +is_a: NCBITaxon:78536 ! Euphyllophyta + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +is_a: NCBITaxon:33208 ! Metazoa + +[Term] +id: NCBITaxon:7711 +name: Chordata +synonym: "chordates" EXACT genbank_common_name [] +synonym: "chordates" RELATED blast_name [] +is_a: NCBITaxon:33511 ! Deuterostomia + +[Term] +id: NCBITaxon:7742 +name: Vertebrata +synonym: "Vertebrata" EXACT scientific_name [] +synonym: "vertebrates" EXACT genbank_common_name [] +synonym: "vertebrates" RELATED blast_name [] +is_a: NCBITaxon:89593 ! Craniata + +[Term] +id: NCBITaxon:7776 +name: Gnathostomata +synonym: "Gnathostomata" EXACT scientific_name [] +synonym: "jawed vertebrates" EXACT genbank_common_name [] +is_a: NCBITaxon:7742 ! Vertebrata + +[Term] +id: NCBITaxon:78536 +name: Euphyllophyta +synonym: "euphyllophytes" RELATED synonym [] +is_a: NCBITaxon:58023 ! Tracheophyta + +[Term] +id: NCBITaxon:8287 +name: Sarcopterygii +is_a: NCBITaxon:117571 ! Euteleostomi + +[Term] +id: NCBITaxon:89593 +name: Craniata +synonym: "Craniata" EXACT scientific_name [] +is_a: NCBITaxon:7711 ! Chordata + +[Term] +id: NCBITaxon:9347 +name: Eutheria +synonym: "eutherian mammals" EXACT common_name [] +synonym: "placental mammals" EXACT common_name [] +synonym: "Placentalia" RELATED synonym [] +synonym: "placentals" EXACT genbank_common_name [] +synonym: "placentals" RELATED blast_name [] +is_a: NCBITaxon:32525 ! Theria + +[Term] +id: NCBITaxon:9443 +name: Primates +synonym: "Primata" RELATED synonym [] +synonym: "primate" EXACT equivalent_name [] +synonym: "primates" RELATED blast_name [] +is_a: NCBITaxon:314146 ! Euarchontoglires + +[Term] +id: NCBITaxon:9526 +name: Catarrhini +is_a: NCBITaxon:314293 ! Simiiformes + +[Term] +id: NCBITaxon:9604 +name: Hominidae +synonym: "great apes" EXACT genbank_common_name [] +synonym: "Pongidae" RELATED synonym [] +is_a: NCBITaxon:314295 ! Hominoidea + +[Term] +id: NCBITaxon:9605 +name: Homo +synonym: "humans" EXACT common_name [] +is_a: NCBITaxon:207598 ! Homininae + +[Term] +id: NCBITaxon:9606 +name: Homo sapiens +synonym: "human" EXACT genbank_common_name [] +synonym: "man" EXACT common_name [] +is_a: NCBITaxon:9605 ! Homo + diff --git a/imports/ncbitaxon_import.owl b/imports/ncbitaxon_import.owl index c1a95c7..3211368 100644 --- a/imports/ncbitaxon_import.owl +++ b/imports/ncbitaxon_import.owl @@ -1,13 +1,15 @@ - + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + @@ -1144,5 +1146,5 @@ - + diff --git a/imports/pato_import.obo b/imports/pato_import.obo new file mode 100644 index 0000000..0ad1915 --- /dev/null +++ b/imports/pato_import.obo @@ -0,0 +1,97 @@ +format-version: 1.2 +data-version: pco/releases/2020-02-13/pato_import.obo +ontology: pco/imports/pato_import.obo + +[Term] +id: PATO:0000001 +name: quality +namespace: quality +alt_id: PATO:0000072 +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +synonym: "trait" EXACT [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000161 +name: rate +namespace: quality +def: "A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time." [PATOC:melissa] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002062 ! physical quality of a process +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001236 +name: process quality +namespace: quality +alt_id: PATO:0001239 +alt_id: PATO:0001240 +def: "A quality which inheres in an process." [PATOC:GVG] +comment: See comments of relational quality of a physical entity. +synonym: "quality of a process" EXACT [] +synonym: "quality of occurrent" EXACT [] +synonym: "quality of process" EXACT [] +synonym: "relational quality of occurrent" EXACT [] +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001241 +name: physical object quality +namespace: quality +alt_id: PATO:0001237 +alt_id: PATO:0001238 +def: "A quality which inheres in a continuant." [PATOC:GVG] +comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. +synonym: "monadic quality of a continuant" EXACT [] +synonym: "monadic quality of an object" NARROW [] +synonym: "monadic quality of continuant" NARROW [] +synonym: "multiply inhering quality of a physical entity" EXACT [] +synonym: "quality of a continuant" EXACT [] +synonym: "quality of a single physical entity" EXACT [] +synonym: "quality of an object" EXACT [] +synonym: "quality of continuant" EXACT [] +xref: snap:Quality +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001338 +name: mixed sex +namespace: quality +def: "A biological sex quality inhering in a population of multiple sexes." [MGED:MGED] +comment: For example a mixture of females and male or males and hermaphrodites. +subset: value_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001415 +name: morbidity +namespace: quality +def: "A quality inhering in a population by virtue of the proportion of its members that are ill at a given time." [PATOC:GVG] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002003 +name: population quality +namespace: quality +def: "A quality that inheres in an entire population or part of a population." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002062 +name: physical quality of a process +namespace: quality +subset: attribute_slim +is_a: PATO:0001236 ! process quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +created_by: george +creation_date: 2009-06-05T09:16:46Z + diff --git a/imports/pato_import.owl b/imports/pato_import.owl index 3ac76b2..a6894b8 100644 --- a/imports/pato_import.owl +++ b/imports/pato_import.owl @@ -1,14 +1,16 @@ - + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + @@ -25,25 +27,116 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -62,7 +155,11 @@ A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATO:0000072 trait + quality + PATO:0000001 + quality @@ -74,29 +171,16 @@ - - - - - A composite chromatic quality composed of hue, saturation and intensity parts. - colour - relative color - color - - - - - A composite chromatic quality composed of hue, saturation and intensity parts. - PATOC:GVG - - - - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + rate @@ -108,48 +192,21 @@ - - - - - A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers. - red - - - - - A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers. - Dictionary:http://dictionary.reference.com/ - - - - - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - relational physical quality - physical quality - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATOC:GVG - - - - A quality which inheres in an process. + PATO:0001239 + PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent + quality + PATO:0001236 + See comments of relational quality of a physical entity. + process quality @@ -166,6 +223,9 @@ A quality which inheres in a continuant. + PATO:0001237 + PATO:0001238 + snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant @@ -174,6 +234,10 @@ quality of continuant monadic quality of an object monadic quality of continuant + quality + PATO:0001241 + Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. + physical object quality @@ -185,43 +249,16 @@ - - - - - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - electromagnetic (EM) radiation quality - - - - - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation - - - - - - - - - An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. - optical quality - - - - - An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. - PATOC:GVG - - - - A biological sex quality inhering in a population of multiple sexes. + quality + PATO:0001338 + + For example a mixture of females and male or males and hermaphrodites. + mixed sex @@ -238,6 +275,11 @@ A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. + quality + PATO:0001415 + + + morbidity @@ -249,27 +291,15 @@ - - - - - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. - radiation quality - - - - - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. - PATOC:GVG - - - - A quality that inheres in an entire population or part of a population. + quality + PATO:0002003 + + population quality @@ -285,11 +315,17 @@ + george + 2009-06-05T09:16:46Z + quality + PATO:0002062 + + physical quality of a process - + diff --git a/imports/ro_import.obo b/imports/ro_import.obo new file mode 100644 index 0000000..339d156 --- /dev/null +++ b/imports/ro_import.obo @@ -0,0 +1,1321 @@ +format-version: 1.2 +data-version: pco/releases/2020-02-13/ro_import.owl +ontology: pco/imports/ro_import +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: ()\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +disjoint_from: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000002 ! part of continuant +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: BFO:0000050 BFO:0000003 ! part of occurrent +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000004 ! part of independent continuant +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000019 ! part of quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant +relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: GO:0003674 +name: molecular_function +is_a: BFO:0000015 ! process +property_value: IAO:0000589 "molecular process" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0003824 +name: catalytic activity +is_a: GO:0003674 ! molecular_function +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0008150 +name: biological_process +is_a: BFO:0000015 ! process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016301 +name: kinase activity +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016740 +name: transferase activity +is_a: GO:0003824 ! catalytic activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +is_a: GO:0016740 ! transferase activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000050 BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +is_a: RO:0002314 ! inheres in part of +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: BFO:0000051 RO:0000057 + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000111 "is location of" xsd:string +property_value: IAO:0000112 "my head is the location of my brain" xsd:string +property_value: IAO:0000112 "this cage is the location of this rat" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000118 "location_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001018 +name: contained in +subset: ro-eco +property_value: IAO:0000111 "contained in" xsd:string +property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string +property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string +property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string +property_value: IAO:0000118 "contained_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0001025 BFO:0000050 +inverse_of: RO:0001019 ! contains + +[Typedef] +id: RO:0001019 +name: contains +subset: ro-eco +property_value: IAO:0000111 "contains" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string +property_value: IAO:0000111 "located in" xsd:string +property_value: IAO:0000112 "my brain is located in my head" xsd:string +property_value: IAO:0000112 "this rat is located in this cage" xsd:string +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000118 "located_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true + +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002019 +name: has ligand +def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002233 ! has input +created_by: dos +creation_date: 2017-07-19T17:30:36Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_functional: true +is_a: RO:0002017 ! has component activity +is_a: RO:0002211 ! regulates +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +holds_over_chain: BFO:0000050 BFO:0000050 +holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 RO:0002131 +is_a: RO:0002323 ! mereotopologically related to +transitive_over: BFO:0000050 ! part of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002180 +name: has component +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002211 +name: regulates +def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string +property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002215 +name: capable of +def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of +expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process +expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002217 +name: actively participates in +def: "x actively participates in y if and only if x participates in y and x realizes some active role" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "agent in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000056 ! participates in +inverse_of: RO:0002218 ! obsolete has active participant + +[Typedef] +id: RO:0002218 +name: obsolete has active participant +def: "x has participant y if and only if x realizes some active role that inheres in y" [] +subset: ro-eco +property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has agent" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000057 ! has participant +is_obsolete: true + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002233 +name: has input +def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "consumes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002314 +name: inheres in part of +def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002502 ! depends on +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002321 +name: ecologically related to +def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] +subset: ro-eco +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002327 +name: enables +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: BFO:0000051 ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 BFO:0000050 +is_a: RO:0002217 ! actively participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "regulated by (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000050 ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002379 +name: spatially coextensive with +def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] +property_value: IAO:0000112 "A lump of clay and a statue" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +synonym: "affects" RELATED [] +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "involved in or reguates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "executes activity in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso ECO:0000353 +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: activity directly regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002449 +name: activity directly negatively regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "inhibits" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002448 ! activity directly regulates activity of + +[Typedef] +id: RO:0002450 +name: activity directly positively regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "activates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002448 ! activity directly regulates activity of + +[Typedef] +id: RO:0002464 +name: helper property (not for use in curation) +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} + +[Typedef] +id: RO:0002481 +name: is kinase activity +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002502 +name: depends on +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso BFO:0000169 + +[Typedef] +id: RO:0002506 +name: causal relation between material entities +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (material entity to material entity)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002506 ! causal relation between material entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002563 +name: interaction relation helper property +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +is_a: RO:0002464 ! helper property (not for use in curation) + +[Typedef] +id: RO:0002564 +name: molecular interaction relation helper property +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002566 +name: causally influences +def: "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (material entity to material entity)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002506 ! causal relation between material entities + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: BFO:0000051 RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 BFO:0000051 +is_a: RO:0002328 ! functionally related to +created_by: cjm +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: cjm +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: cjm +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:19Z + diff --git a/imports/ro_import.owl b/imports/ro_import.owl index f22a95b..df06d81 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -1,17 +1,22 @@ - + xmlns:swrl="http://www.w3.org/2003/11/swrl#" + xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" + xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" + xmlns:terms="http://purl.org/dc/terms/" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + + @@ -28,91 +33,338 @@ - + + + - + + + - + + + - + + + - + + + + editor note + - + + + - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + - + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + + is a defining property chain axiom + - + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -145,7 +397,17 @@ A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of + + + + + + + + part of + + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -168,6 +430,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part + has part @@ -191,6 +454,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by @@ -209,6 +474,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes @@ -252,6 +519,42 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + + bearer of + + + + @@ -264,6 +567,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in + participates in @@ -286,16 +590,162 @@ A continuant cannot have an occurrent as part: use 'participates in'. Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + + quality of + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + + has quality + + + + + + + + + + is location of + my head is the location of my brain + this cage is the location of this rat + a relation between two independent continuants, the location and the target, in which the target is entirely within the location + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + location_of + + + location of + + + + + + + + + + + + + + + contained in + Containment is location not involving parthood, and arises only where some immaterial continuant is involved. + Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): + Intended meaning: +domain: material entity +range: spatial region or site (immaterial continuant) + + contained_in + + + + contained in + + + + + + + + contains + + + + contains + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + + located in + + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + + has regulatory component activity @@ -305,6 +755,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + + has negative regulatory component activity @@ -314,6 +770,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + + has positive regulatory component activity @@ -322,6 +784,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + + has component activity @@ -330,6 +797,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + + has component process @@ -338,7 +812,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + + has ligand @@ -348,7 +826,18 @@ A continuant cannot have an occurrent as part: use 'participates in'. + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + directly regulated by + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + @@ -357,7 +846,18 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + + directly negatively regulated by + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + @@ -366,7 +866,18 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + + directly positively regulated by + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + @@ -376,7 +887,19 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + + has effector activity + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + @@ -386,7 +909,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. David Osumi-Sutherland + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after @@ -400,6 +925,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by @@ -412,7 +938,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. David Osumi-Sutherland ends_at_start_of meets + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes @@ -434,6 +963,17 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + overlaps @@ -451,6 +991,15 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + + has component + @@ -467,6 +1016,19 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + regulates @@ -477,6 +1039,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + + negatively regulates @@ -492,6 +1061,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + + positively regulates @@ -502,6 +1078,18 @@ A continuant cannot have an occurrent as part: use 'participates in'. + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + + capable of @@ -515,6 +1103,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + + capable of part of + @@ -528,6 +1123,38 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + x actively participates in y if and only if x participates in y and x realizes some active role + Chris Mungall + agent in + + actively participates in + + + + + + + + + 'heart development' has active participant some Shh protein + + x has participant y if and only if x realizes some active role that inheres in y + This may be obsoleted and replaced by the original 'has agent' relation + Chris Mungall + has agent + + + obsolete has active participant + true + + + + @@ -536,7 +1163,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -549,6 +1180,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + Chris Mungall + consumes + + + has input @@ -561,6 +1199,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + + acts upstream of + @@ -573,6 +1216,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + + acts upstream of or within + @@ -581,6 +1230,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + + causally upstream of, positive effect @@ -589,23 +1244,77 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + causally upstream of, negative effect - + - + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of inheres in part of + Chris Mungall + + + + inheres in part of + + + + + + + + + + true + - + - + + A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + + + ecologically related to + - + + + + A mereological relationship or a topological relationship + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + + mereotopologically related to + + + + + @@ -618,13 +1327,30 @@ A continuant cannot have an occurrent as part: use 'participates in'. + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + + enables - + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + + functionally related to + @@ -636,6 +1362,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + + part of structure that is capable of @@ -652,6 +1383,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -661,6 +1393,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + + involved in + @@ -668,12 +1407,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + - - - - - + inverse of enables + Chris Mungall + + enabled by @@ -685,6 +1424,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + inverse of regulates + Chris Mungall + regulated by (processual) + + + regulated by @@ -693,6 +1438,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + inverse of negatively regulates + Chris Mungall + + + negatively regulated by @@ -701,6 +1451,42 @@ A continuant cannot have an occurrent as part: use 'participates in'. + inverse of positively regulates + Chris Mungall + + + positively regulated by + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + + has member @@ -710,6 +1496,32 @@ A continuant cannot have an occurrent as part: use 'participates in'. + inverse of has input + Chris Mungall + + + + input of + + + + + + + + + + + + + + + A lump of clay and a statue + x spatially_coextensive_with y if and inly if x and y have the same location + Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios + + spatially coextensive with @@ -720,6 +1532,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + inverse of upstream of + Chris Mungall + + causally downstream of @@ -730,6 +1547,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + Chris Mungall + + immediately causally downstream of @@ -737,7 +1558,27 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + + This relation groups causal relations between material entities and causal relations between processes + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causally related to @@ -748,6 +1589,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + + causally upstream of @@ -757,6 +1603,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + + immediately causally upstream of @@ -767,6 +1619,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + + causally upstream of or within @@ -776,6 +1635,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + inverse of causally upstream of or within + Chris Mungall + + + + causally downstream of or within @@ -793,6 +1658,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + + involved in regulation of @@ -809,6 +1678,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + + involved in positive regulation of @@ -825,6 +1699,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + + involved in negative regulation of @@ -835,6 +1714,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union + Chris Mungall + involved in or reguates + + involved in or involved in regulation of @@ -848,6 +1733,14 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + Chris Mungall + executes activity in + enables activity in + + + is active in @@ -858,6 +1751,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. true + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + @@ -867,6 +1767,17 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + Considering relabeling as 'pairwise interacts with' + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations @@ -876,34 +1787,27 @@ A continuant cannot have an occurrent as part: use 'participates in'. + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + Chris Mungall + binds + molecularly binds with + + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 - - - - - - - - - - - - - + - - - - - - - - - - + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + + phosphorylates @@ -918,6 +1822,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + Chris Mungall + molecularly controls + + activity directly regulates activity of @@ -931,6 +1840,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + Chris Mungall + inhibits + molecularly decreases activity of + + activity directly negatively regulates activity of @@ -944,44 +1859,23 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - - - - - - - - - - + Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + Chris Mungall + activates + molecularly increases activity of + + activity directly positively regulates activity of - - - - - - - - + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + + helper property (not for use in curation) @@ -995,6 +1889,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + Chris Mungall + + + has part that occurs in @@ -1008,11 +1907,26 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + Chris Mungall + + is kinase activity + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + + causal agent in process @@ -1023,6 +1937,23 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between processes + + + + + + + + Chris Mungall + + depends on + @@ -1033,6 +1964,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between material entities @@ -1042,6 +1979,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Chris Mungall + + causally influenced by (material entity to material entity) + + causally influenced by @@ -1050,6 +1992,22 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Chris Mungall + + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + + molecular interaction relation helper property @@ -1068,14 +2026,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - + Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b + Chris Mungall + + causally influences (material entity to material entity) + + causally influences @@ -1085,6 +2041,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + + directly regulates @@ -1098,6 +2061,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + Chris Mungall + + has part structure that is capable of @@ -1108,6 +2076,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + Chris Mungall + + + causal relation between material entity and a process @@ -1120,6 +2094,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + + capable of regulating @@ -1132,6 +2111,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + + capable of negatively regulating @@ -1144,6 +2127,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + + capable of positively regulating @@ -1152,21 +2140,25 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Inverse of 'causal agent in process' + + + process has causal agent - - - - - - + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + + directly positively regulates @@ -1176,6 +2168,130 @@ A continuant cannot have an occurrent as part: use 'participates in'. + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + + directly negatively regulates + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + cjm + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + cjm + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + + causally upstream of or within, positive effect @@ -1194,6 +2310,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + @@ -1202,6 +2324,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant @@ -1210,6 +2333,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + @@ -1217,6 +2346,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent @@ -1226,45 +2356,125 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + spatial region + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + + + quality + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + + specifically dependent continuant + + + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + + + + immaterial entity + + + + + molecular process + molecular_function - + - - receptor activity + + + + catalytic activity @@ -1273,14 +2483,53 @@ A continuant cannot have an occurrent as part: use 'participates in'. + biological_process - + - + + + + + + true + + + + kinase activity + + + + + + + + + + transferase activity + + + + + + + + + + transferase activity, transferring phosphorus-containing groups + + + + + + + + + @@ -1336,6 +2585,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. /////////////////////////////////////////////////////////////////////////////////////// --> + + + + + + @@ -1354,6 +2609,18 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + @@ -1378,6 +2645,132 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' @@ -1497,7 +2890,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - From ligand activity to has_ligand @@ -1505,9 +2897,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -1515,10 +2907,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -1526,12 +2917,26 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + - + + + + + + + + + + + + + + @@ -1544,9 +2949,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -1773,63 +3178,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - From has_ligand to ligand activity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input @@ -2056,6 +3404,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -2063,7 +3412,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -2074,9 +3423,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -2085,17 +3434,84 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2108,8 +3524,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -2119,8 +3535,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -2144,9 +3560,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg @@ -2154,9 +3567,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -2165,36 +3578,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -2205,9 +3594,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -2218,5 +3607,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/pco-base.obo b/pco-base.obo new file mode 100644 index 0000000..1c082c0 --- /dev/null +++ b/pco-base.obo @@ -0,0 +1,493 @@ +format-version: 1.2 +data-version: pco/releases/2020-02-13/pco-base.owl +remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. +ontology: pco/pco-base +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string +property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string +property_value: http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 xsd:string + +[Term] +id: CARO:0001010 +name: organism or virus or viroid +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +is_a: BFO:0000040 +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "organism or virus" xsd:string + +[Term] +id: CARO:0010004 +name: organism +def: "An individual member of a clade." [] +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +is_a: CARO:0001010 ! organism or virus or viroid +property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string +property_value: IAO:0000589 "organism" xsd:string + +[Term] +id: GO:0051704 +is_a: BFO:0000015 + +[Term] +id: IAO:0000030 +is_a: BFO:0000031 + +[Term] +id: PCO:0000000 +name: collection of organisms +def: "A material entity that consists of two or more organisms, viruses, or viroids." [] +comment: May be of the same or different species. +is_a: BFO:0000027 +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid +property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "group of organism" xsd:string +property_value: IAO:0000118 "organism collection" xsd:string + +[Term] +id: PCO:0000001 +name: population of organisms +def: "A collection of organisms, all of the same species, that live in the same place." [] +comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000112 "" xsd:string +property_value: IAO:0000112 "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 ISBN:0878932739 xsd:string + +[Term] +id: PCO:0000002 +name: ecological community +def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] +comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +property_value: IAO:0000118 "multispecies community" xsd:string +property_value: IAO:0000119 ISBN:0865423504 xsd:string + +[Term] +id: PCO:0000003 +name: quality of a population +def: "A quality that inheres in a biological population." [] +comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. +intersection_of: PATO:0002003 +intersection_of: RO:0000052 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000004 +name: quality of an ecological community +def: "A quality that inheres in a community." [] +comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. +intersection_of: PATO:0002003 +intersection_of: RO:0000052 PCO:0000002 ! ecological community +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000005 +name: population process +def: "A process that has as primary participant a population. " [] +comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +is_a: BFO:0000015 +relationship: RO:0000057 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000006 +name: population birth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000007 +name: population death rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000008 +name: population growth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string + +[Term] +id: PCO:0000009 +name: obsolete carrying capacity +def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] +is_a: ObsoleteClass +property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +property_value: IAO:0000119 ISBN:0878932739 xsd:string +property_value: IAO:0000231 IAO:0000423 +is_obsolete: true + +[Term] +id: PCO:0000010 +name: community species richness +def: "The number of different species represented in an ecological community." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string + +[Term] +id: PCO:0000011 +name: population growth +def: "A process that leads to a change in the number of individuals (positive or negative) in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000012 +name: logistic population growth +def: "A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000013 +name: exponential population growth +def: "A population growth process that leads to an exponential increase in the number of individuals in a population." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000014 +name: predator role +is_a: BFO:0000023 +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000015 +name: prey role +is_a: BFO:0000023 +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000016 +name: symbiont role +is_a: BFO:0000023 +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000017 +name: species as a collection of organisms +def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string + +[Term] +id: PCO:0000018 +name: single-species collection of organisms +def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000118 "collection of organisms of the same species" xsd:string + +[Term] +id: PCO:0000019 +name: community species diversity +def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] +comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string + +[Term] +id: PCO:0000020 +name: family +def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] +comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string +property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string + +[Term] +id: PCO:0000021 +name: population extinction +def: "A population process that ultimately leads to the death of all individuals in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000022 +name: species extinction +def: "A process that ultimately leads to the death of all individuals in a population." [] +is_a: BFO:0000015 +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000023 +name: community species evenness +def: "A quality of a community that reflects how close in abundance all species in a community are." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_evenness" xsd:string + +[Term] +id: PCO:0000024 +name: household +def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] +is_a: PCO:0000031 ! organismal entity +relationship: RO:0002321 ENVO:01000744 +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string + +[Term] +id: PCO:0000025 +name: red population +comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000026 +name: red organism +comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000027 +name: collection of humans +def: "A collection of organisms of the same species that has as members only humans." [] +is_a: PCO:0000018 ! single-species collection of organisms +intersection_of: PCO:0000018 ! single-species collection of organisms +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "human community" xsd:string +property_value: IAO:0000118 "human population" xsd:string + +[Term] +id: PCO:0000028 +name: community +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). +is_a: ObsoleteClass +property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000029 +name: multi-species collection of organisms +def: "A collection of organisms that consists of two or more organisms from at least two species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string + +[Term] +id: PCO:0000030 +name: agricultural household +name: obsolete organismal entity +def: "A household in which the majority of the income of its members is derived from agricultural activities." [] +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: ObsoleteClass +is_a: PCO:0000024 ! household +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string +property_value: IAO:0000231 "wrong IRI form" xsd:string +is_obsolete: true +replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 + +[Term] +id: PCO:0000031 +name: organismal entity +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: BFO:0000040 +union_of: CARO:0001010 ! organism or virus or viroid +union_of: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 + +[Term] +id: PCO:0000032 +name: biological family +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +is_a: PCO:0000020 ! family +property_value: IAO:0000118 "genealogical family" xsd:string +property_value: IAO:0000119 "Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/" xsd:string + +[Term] +id: PCO:0000033 +name: human social gathering activity +def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] +is_a: GO:0035176 +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000034 +name: human community event +def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000035 +name: party +def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000037 +name: potluck +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string +property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000038 +name: wedding +def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000039 +name: baby shower +def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000040 +name: tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: PCO:0000002 ! ecological community +relationship: BFO:0000050 ENVO:01001369 +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string + +[Term] +id: PCO:0000041 +name: invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: PATO:0001241 + +[Term] +id: PCO:0000042 +name: microbe +synonym: "microbial organism" EXACT [] +is_a: CARO:0001010 ! organism or virus or viroid +relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye + +[Term] +id: PCO:0000043 +name: collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe +intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000044 +name: multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: PCO:0000029 ! multi-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000045 +name: single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000046 +name: microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: PCO:0000001 ! population of organisms +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0001000 +name: pair of interacting organisms +def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] +is_a: BFO:0000040 +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid + +[Term] +id: PCO:0001001 +name: pair of interacting organisms of the same species +is_a: PCO:0001000 ! pair of interacting organisms + +[Term] +id: PCO:1000000 +name: migratory population +def: "A population which is participating in a migration process." [] +is_a: PCO:0000001 ! population of organisms +relationship: RO:0000056 PCO:1000001 ! population migration +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:1000001 +name: population migration +def: "A population process during which a population moves from one area to another." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Migration xsd:string + +[Term] +id: PCO:1000002 +name: human population migration +def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration +is_a: PCO:1000001 ! population migration +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000003 +name: human migratory population +def: "A migratory population of humans, travelling with the intention of settling in a new area." [] +is_a: PCO:0000027 ! collection of humans +relationship: RO:0000056 PCO:1000002 ! human population migration +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000004 +name: microbial community +def: "An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness." [] +comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. +synonym: "microbiota" BROAD [] +is_a: PCO:0000002 ! ecological community +is_a: PCO:0000044 ! multi-species collection of microbes +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string +property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string + diff --git a/pco-base.owl b/pco-base.owl new file mode 100644 index 0000000..37a491e --- /dev/null +++ b/pco-base.owl @@ -0,0 +1,1244 @@ + + + + + http://orcid.org/0000-0002-4366-3088 + https://orcid.org/0000-0001-8815-0078 + David Osumi-Sutherland + Jie Zheng + Pier Luigi Buttigieg + Ramona Walls + http://creativecommons.org/publicdomain/zero/1.0/ + http://purl.obolibrary.org/obo/IAO_8000001 + The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + organism or virus + Melissa Haendel + 9/18/11 + organism or virus or viroid + + + + + + + + + An individual member of a clade. + organism + mah + 7.16.2011 + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + organism + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. + + A material entity that consists of two or more organisms, viruses, or viroids. + group of organism + organism collection + May be of the same or different species. + collection of organisms + + + + + + + + + + This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed. + + A collection of organisms, all of the same species, that live in the same place. + ISBN:0878932739 + It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. + +Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. + population of organisms + + + + + + + + + + + + + + 2 + + + + + + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. + multispecies community + ISBN:0865423504 + Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. + ecological community + + + + + + + + + + + + + + + + + + + + A quality that inheres in a biological population. + See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. + quality of a population + + + + + + + + + + + + + + + + + + + + A quality that inheres in a community. + These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. + quality of an ecological community + + + + + + + + + + + + + + + + A process that has as primary participant a population. + Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + population process + + + + + + + + + + population birth rate + + + + + + + + + + population death rate + + + + + + + + + + Is a rate a quality? Population growth rate may be better classified as a process profile. + population growth rate + + + + + + + + + The maximum number of individuals that can be supported in a population that is growing according to logistic growth. + Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE. + ISBN:0878932739 + + obsolete carrying capacity + true + + + + + + + + + + The number of different species represented in an ecological community. + This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019). + adapted from http://en.wikipedia.org/wiki/Species_richness + community species richness + + + + + + + + + + A process that leads to a change in the number of individuals (positive or negative) in a population. + population growth + + + + + + + + + + A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat. + logistic population growth + + + + + + + + + + A population growth process that leads to an exponential increase in the number of individuals in a population. + exponential population growth + + + + + + + + + + predator role + + + + + + + + + + prey role + + + + + + + + + + symbiont role + + + + + + + + + + A collection of organisms that has as parts every organism of given species and no organisms of any other species. + At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. + species as a collection of organisms + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + + A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. + collection of organisms of the same species + single-species collection of organisms + + + + + + + + + + The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness. + If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity. + adapted from http://en.wikipedia.org/wiki/Species_diversity + The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. + community species diversity + + + + + + + + + + A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. + Needs axioms for family relationships. + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 + Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. + family + + + + + + + + + + A population process that ultimately leads to the death of all individuals in a population. + population extinction + + + + + + + + + + A process that ultimately leads to the death of all individuals in a population. + species extinction + + + + + + + + + If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. + + A quality of a community that reflects how close in abundance all species in a community are. + adapted from http://en.wikipedia.org/wiki/Species_evenness + community species evenness + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. + Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household + household + + + + + + + + + + This is an example population added to demonstrate the modeling pattern for collections of organisms. + red population + true + + + + + + + + + + An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. + red organism + true + + + + + + + + + + + + + + + + + + 2 + + + + + + + + A collection of organisms of the same species that has as members only humans. + human community + human population + collection of humans + + + + + + + + + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. + Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. + + These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). + community + true + + + + + + + + + + A collection of organisms that consists of two or more organisms from at least two species. + Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". + + multi-species collection of organisms + + + + + + + + + + A household in which the majority of the income of its members is derived from agricultural activities. + This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term. + agricultural household + + + + + + + + + + + + + + + + + + A material entity that is one or more organisms, viruses or viroids. + organismal entity + + + + + + + + + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. + genealogical family + Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/ + biological family + + + + + + + + + + + + + + + A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. + Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029 + GenEpiO curators + human social gathering activity + + + + + + + + + A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034 + GenEpio curators + human community event + + + + + + + + + A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030 + GenEpiO curators + party + + + + + + + + + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. + GenEpio curators + potluck + + + + + + + + + A human social gathering at which two people are married. May include a legal or social ceremony. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 + GenEpio curators + wedding + + + + + + + + + A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 + GenEpiO curators + baby shower + + + + + + + + + + + + + + + + + + 2 + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + + + + + + + 1 + + + + + + + + + pair of interacting organisms of the same species + + + + + + + + + + + + + + + + A population which is participating in a migration process. + migratory population + + + + + + + + + + A population process during which a population moves from one area to another. + https://en.wikipedia.org/wiki/Migration + The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. + population migration + + + + + + + + + + + + + + + + A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location. + https://en.wikipedia.org/wiki/Human_migration + The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration + human population migration + + + + + + + + + + + + + + + + A migratory population of humans, travelling with the intention of settling in a new area. + https://en.wikipedia.org/wiki/Human_migration + human migratory population + + + + + + + + + + + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. + A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 + http://orcid.org/0000-0002-4366-3088 + http://dx.doi.org/10.1038/ismej.2009.88 + microbiota + The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. + microbial community + + + + + + + + + A material entity that is one or more organisms, viruses or viroids. + wrong IRI form + http://purl.obolibrary.org/obo/PCO_0000031 + obsolete organismal entity + true + + + + + + + + + + + + + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community + + + + + + + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + + + + + + + microbial organism + microbe + + + + + + + + + + + + + + + + + 2 + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + diff --git a/pco-full.obo b/pco-full.obo new file mode 100644 index 0000000..84df48c --- /dev/null +++ b/pco-full.obo @@ -0,0 +1,1820 @@ +format-version: 1.2 +data-version: pco/releases/2020-02-13/pco-full.owl +remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. +ontology: pco/pco-full +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string +property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: BFO:0000179 "continuant" xsd:string +property_value: BFO:0000180 "Continuant" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: BFO:0000179 "occurrent" xsd:string +property_value: BFO:0000180 "Occurrent" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "ic" xsd:string +property_value: BFO:0000180 "IndependentContinuant" xsd:string +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +is_a: BFO:0000003 ! occurrent +property_value: BFO:0000179 "process" xsd:string +property_value: BFO:0000180 "Process" xsd:string +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +is_a: BFO:0000020 ! specifically dependent continuant +property_value: BFO:0000179 "realizable" xsd:string +property_value: BFO:0000180 "RealizableEntity" xsd:string +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "sdc" xsd:string +property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +is_a: BFO:0000017 ! realizable entity +property_value: BFO:0000179 "role" xsd:string +property_value: BFO:0000180 "Role" xsd:string +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000027 +name: object aggregate +is_a: BFO:0000040 ! material entity +property_value: BFO:0000179 "object-aggregate" xsd:string +property_value: BFO:0000180 "ObjectAggregate" xsd:string +property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string +property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string +property_value: IAO:0000112 "a symphony orchestra" xsd:string +property_value: IAO:0000112 "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)" xsd:string +property_value: IAO:0000112 "defined by fiat: the aggregate of members of an organization" xsd:string +property_value: IAO:0000112 "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string +property_value: IAO:0000112 "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string +property_value: IAO:0000112 "defined via attributive delimitations such as: the patients in this hospital" xsd:string +property_value: IAO:0000112 "the aggregate of bearings in a constant velocity axle joint" xsd:string +property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:string +property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string +property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string +property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string +property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} +property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000029 +name: site +is_a: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "site" xsd:string +property_value: BFO:0000180 "Site" xsd:string +property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string +property_value: IAO:0000112 "a rabbit hole" xsd:string +property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string +property_value: IAO:0000112 "Manhattan Canyon)" xsd:string +property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string +property_value: IAO:0000112 "the Grand Canyon" xsd:string +property_value: IAO:0000112 "the hold of a ship" xsd:string +property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string +property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string +property_value: IAO:0000112 "the interior of your bedroom" xsd:string +property_value: IAO:0000112 "the interior of your office" xsd:string +property_value: IAO:0000112 "the interior of your refrigerator" xsd:string +property_value: IAO:0000112 "the lumen of your gut" xsd:string +property_value: IAO:0000112 "the Piazza San Marco" xsd:string +property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string +property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +is_a: BFO:0000002 ! continuant +property_value: BFO:0000179 "gdc" xsd:string +property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "material" xsd:string +property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant +property_value: BFO:0000179 "immaterial" xsd:string +property_value: BFO:0000180 "ImmaterialEntity" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: CARO:0001010 +name: organism or virus or viroid +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +is_a: PCO:0000031 ! organismal entity +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "organism or virus" xsd:string + +[Term] +id: CARO:0010004 +name: organism +def: "An individual member of a clade." [] +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +is_a: CARO:0001010 ! organism or virus or viroid +property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string +property_value: IAO:0000589 "organism" xsd:string + +[Term] +id: DbXref +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Definition +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: ENVO:00000070 +name: construction +def: "A feature that has been constructed by deliberate human effort." [MA:ma] +synonym: "constructed feature" EXACT [] +is_a: ENVO:01000813 ! astronomical body part +property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string + +[Term] +id: ENVO:00002297 +name: environmental feature +namespace: ENVO +def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] +comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. +is_a: BFO:0000040 ! material entity + +[Term] +id: ENVO:01000254 +name: environmental system +def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +synonym: "environment" EXACT [] +xref: EcoLexicon:environment +is_a: BFO:0000040 ! material entity +creation_date: 2013-09-23T16:04:08Z + +[Term] +id: ENVO:01000744 +name: human dwelling +def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] +is_a: ENVO:00000070 ! construction +property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string + +[Term] +id: ENVO:01000813 +name: astronomical body part +def: "A material part of an astronomical body." [] +subset: envoAstro +subset: envoPolar +is_a: ENVO:00002297 ! environmental feature + +[Term] +id: ENVO:01001369 +name: tidal mangrove shrubland +alt_id: CMECS:577 +def: "A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas." [] +comment: This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" +subset: envoCmecs +subset: envoMarine +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ENVO:01000254 ! environmental system +created_by: http://orcid.org/0000-0002-4366-3088 + +[Term] +id: GO:0007610 +name: behavior +namespace: biological_process +alt_id: GO:0044708 +def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] +comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). +subset: gocheck_do_not_manually_annotate +subset: goslim_agr +subset: goslim_flybase_ribbon +synonym: "behavioral response to stimulus" EXACT [] +synonym: "behaviour" EXACT [] +synonym: "behavioural response to stimulus" EXACT [] +synonym: "single-organism behavior" RELATED [] +xref: Wikipedia:Behavior +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-20T14:06:08Z + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0035176 +name: social behavior +namespace: biological_process +def: "Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group." [GOC:jh2, PMID:12848939, Wikipedia:Social_behavior] +comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. +synonym: "cooperative behavior" RELATED [] +synonym: "social behaviour" EXACT [] +xref: Wikipedia:Social_behavior +is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051705 ! multi-organism behavior +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0044419 +name: interspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +subset: goslim_candida +subset: goslim_pir +synonym: "interaction with another species" EXACT [] +synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051703 +name: intraspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: goslim_pir +synonym: "intraspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051704 +name: multi-organism process +namespace: biological_process +alt_id: GO:0051706 +def: "A biological process which involves another organism of the same or different species." [GOC:jl] +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "interaction between organisms" EXACT [] +synonym: "physiological interaction between organisms" EXACT [] +synonym: "physiological interaction with other organism" EXACT [] +is_a: BFO:0000015 ! process +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051705 +name: multi-organism behavior +namespace: biological_process +alt_id: GO:0023032 +alt_id: GO:0044709 +def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] +subset: goslim_pir +synonym: "behavioral interaction between organisms" EXACT [] +synonym: "behavioral interaction with other organism" EXACT [] +synonym: "behavioral signaling" NARROW [] +synonym: "behavioral signalling" NARROW [GOC:mah] +synonym: "behavioural interaction between organisms" EXACT [] +synonym: "behavioural interaction with other organism" EXACT [] +is_a: GO:0007610 ! behavior +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: IAO:0000027 +name: data item +is_a: IAO:0000030 ! information content entity + +[Term] +id: IAO:0000030 +name: information content entity +is_a: BFO:0000031 ! generically dependent continuant + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:03Z + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 +created_by: cjm +creation_date: 2018-05-20T20:55:30Z + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "source ontology module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:47Z + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:56:13Z + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies +created_by: cjm +creation_date: 2018-05-20T20:56:23Z + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract +created_by: cjm +creation_date: 2018-05-20T20:56:47Z + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide +created_by: cjm +creation_date: 2018-05-20T20:58:11Z + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:38Z + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:49Z + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "ribbon subset" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:19Z + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "antislim" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:57Z + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000118 "external import" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:00:14Z + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +created_by: cjm +creation_date: 2018-05-20T21:14:16Z + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso http://robot.obolibrary.org/reason +created_by: cjm +creation_date: 2018-05-20T21:20:33Z + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:21:12Z + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ +created_by: cjm +creation_date: 2018-05-20T21:21:21Z + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +created_by: cjm +creation_date: 2018-05-20T21:28:15Z + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-22T04:15:54Z + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: seeAlso "6.2" +created_by: cjm +creation_date: 2018-05-22T04:16:10Z + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +created_by: cjm +creation_date: 2018-05-22T04:16:28Z + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +created_by: cjm +creation_date: 2018-05-22T04:16:48Z + +[Term] +id: NCBITaxon:10239 +name: Viruses +namespace: ncbi_taxonomy +synonym: "Vira" RELATED synonym [] +synonym: "Viridae" RELATED synonym [] +synonym: "viruses" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117570 +name: Teleostomi +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:7776 ! Gnathostomata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117571 +name: Euteleostomi +namespace: ncbi_taxonomy +alt_id: NCBITaxon:40673 +synonym: "bony vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:117570 ! Teleostomi +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:12884 +name: Viroids +namespace: ncbi_taxonomy +synonym: "Viroid" RELATED synonym [] +synonym: "viroids" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131221 +name: Streptophytina +namespace: ncbi_taxonomy +synonym: "Charophyta/Embryophyta group" RELATED synonym [] +synonym: "charophyte/embryophyte group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:35493 ! Streptophyta +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131567 +name: cellular organisms +namespace: ncbi_taxonomy +synonym: "biota" RELATED synonym [] +xref: GC_ID:1 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1338369 +name: Dipnotetrapodomorpha +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:8287 ! Sarcopterygii +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437010 +name: Boreoeutheria +namespace: ncbi_taxonomy +synonym: "Boreotheria" RELATED synonym [] +xref: GC_ID:1 +xref: PMID:11743200 +xref: PMID:11791233 +is_a: NCBITaxon:9347 ! Eutheria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437180 +name: Acrogymnospermae +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2 +name: Bacteria +namespace: ncbi_taxonomy +synonym: "bacteria" RELATED blast_name [] +synonym: "eubacteria" EXACT genbank_common_name [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11542017 +xref: PMID:11542087 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:207598 +name: Homininae +namespace: ncbi_taxonomy +synonym: "Homo/Pan/Gorilla group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:9604 ! Hominidae +property_value: has_rank NCBITaxon:subfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2157 +name: Archaea +namespace: ncbi_taxonomy +synonym: "archaea" RELATED blast_name [] +synonym: "Archaebacteria" RELATED synonym [] +synonym: "Mendosicutes" RELATED synonym [] +synonym: "Metabacteria" RELATED synonym [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11541975 +xref: PMID:11542064 +xref: PMID:11542149 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:25527841 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2759 +name: Eukaryota +namespace: ncbi_taxonomy +synonym: "Eucarya" RELATED synonym [] +synonym: "Eucaryotae" RELATED synonym [] +synonym: "eucaryotes" EXACT genbank_common_name [] +synonym: "Eukarya" RELATED synonym [] +synonym: "Eukaryotae" RELATED synonym [] +synonym: "eukaryotes" EXACT common_name [] +synonym: "eukaryotes" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3041 +name: Chlorophyta +namespace: ncbi_taxonomy +synonym: "algae" RELATED in_part [] +synonym: "Chlorophycota" RELATED synonym [] +synonym: "Chlorophyta sensu Bremer 1985" RELATED synonym [] +synonym: "green algae" EXACT genbank_common_name [] +synonym: "green algae" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314146 +name: Euarchontoglires +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:11214319 +xref: PMID:12082125 +xref: PMID:12878460 +xref: PMID:15522813 +is_a: NCBITaxon:1437010 ! Boreoeutheria +property_value: has_rank NCBITaxon:superorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314293 +name: Simiiformes +namespace: ncbi_taxonomy +synonym: "Anthropoidea" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:376913 ! Haplorrhini +property_value: has_rank NCBITaxon:infraorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314295 +name: Hominoidea +namespace: ncbi_taxonomy +synonym: "ape" EXACT common_name [] +synonym: "apes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9526 ! Catarrhini +property_value: has_rank NCBITaxon:superfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3193 +name: Embryophyta +namespace: ncbi_taxonomy +synonym: "higher plants" EXACT common_name [] +synonym: "land plants" EXACT common_name [] +synonym: "land plants" RELATED blast_name [] +synonym: "plants" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:131221 ! Streptophytina +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32523 +name: Tetrapoda +namespace: ncbi_taxonomy +synonym: "tetrapods" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32524 +name: Amniota +namespace: ncbi_taxonomy +synonym: "amniotes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32523 ! Tetrapoda +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32525 +name: Theria +namespace: ncbi_taxonomy +synonym: "Theria" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:40674 ! Mammalia +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33090 +name: Viridiplantae +namespace: ncbi_taxonomy +synonym: "Chlorobionta" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] +synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "green plants" EXACT common_name [] +synonym: "green plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33154 +name: Opisthokonta +namespace: ncbi_taxonomy +synonym: "Fungi/Metazoa group" RELATED synonym [] +synonym: "opisthokonts" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33208 +name: Metazoa +namespace: ncbi_taxonomy +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33213 +name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:6072 ! Eumetazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33511 +name: Deuterostomia +namespace: ncbi_taxonomy +synonym: "deuterostomes" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33213 ! Bilateria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3398 +name: Magnoliophyta +namespace: ncbi_taxonomy +synonym: "Angiospermae" RELATED synonym [] +synonym: "angiosperms" EXACT common_name [] +synonym: "flowering plants" EXACT genbank_common_name [] +synonym: "flowering plants" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:25249442 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:35493 +name: Streptophyta +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:376913 +name: Haplorrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:9443 ! Primates +property_value: has_rank NCBITaxon:suborder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:40674 +name: Mammalia +namespace: ncbi_taxonomy +synonym: "mammals" EXACT genbank_common_name [] +synonym: "mammals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32524 ! Amniota +property_value: has_rank NCBITaxon:class +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58023 +name: Tracheophyta +namespace: ncbi_taxonomy +synonym: "vascular plants" EXACT common_name [] +synonym: "vascular plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:3193 ! Embryophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58024 +name: Spermatophyta +namespace: ncbi_taxonomy +synonym: "seed plants" EXACT common_name [] +synonym: "seed plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:78536 ! Euphyllophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33208 ! Metazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7711 +name: Chordata +namespace: ncbi_taxonomy +synonym: "chordates" EXACT genbank_common_name [] +synonym: "chordates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33511 ! Deuterostomia +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7742 +name: Vertebrata +namespace: ncbi_taxonomy +synonym: "Vertebrata" EXACT scientific_name [] +synonym: "vertebrates" EXACT genbank_common_name [] +synonym: "vertebrates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:89593 ! Craniata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7776 +name: Gnathostomata +namespace: ncbi_taxonomy +synonym: "Gnathostomata" EXACT scientific_name [] +synonym: "jawed vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7742 ! Vertebrata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:78536 +name: Euphyllophyta +namespace: ncbi_taxonomy +synonym: "euphyllophytes" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:58023 ! Tracheophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:8287 +name: Sarcopterygii +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:117571 ! Euteleostomi +property_value: has_rank NCBITaxon:superclass +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:89593 +name: Craniata +namespace: ncbi_taxonomy +synonym: "Craniata" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7711 ! Chordata +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9347 +name: Eutheria +namespace: ncbi_taxonomy +synonym: "eutherian mammals" EXACT common_name [] +synonym: "placental mammals" EXACT common_name [] +synonym: "Placentalia" RELATED synonym [] +synonym: "placentals" EXACT genbank_common_name [] +synonym: "placentals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32525 ! Theria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9443 +name: Primates +namespace: ncbi_taxonomy +synonym: "Primata" RELATED synonym [] +synonym: "primate" EXACT equivalent_name [] +synonym: "primates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:314146 ! Euarchontoglires +property_value: has_rank NCBITaxon:order +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9526 +name: Catarrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:314293 ! Simiiformes +property_value: has_rank NCBITaxon:parvorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9604 +name: Hominidae +namespace: ncbi_taxonomy +synonym: "great apes" EXACT genbank_common_name [] +synonym: "Pongidae" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:314295 ! Hominoidea +property_value: has_rank NCBITaxon:family +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9605 +name: Homo +namespace: ncbi_taxonomy +synonym: "humans" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:207598 ! Homininae +property_value: has_rank NCBITaxon:genus +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9606 +name: Homo sapiens +namespace: ncbi_taxonomy +synonym: "Home sapiens" RELATED misspelling [] +synonym: "Homo sampiens" RELATED misspelling [] +synonym: "Homo sapeins" RELATED misspelling [] +synonym: "Homo sapian" RELATED misspelling [] +synonym: "Homo sapians" RELATED misspelling [] +synonym: "Homo sapien" RELATED misspelling [] +synonym: "Homo sapience" RELATED misspelling [] +synonym: "Homo sapiense" RELATED misspelling [] +synonym: "Homo sapients" RELATED misspelling [] +synonym: "Homo sapines" RELATED misspelling [] +synonym: "Homo spaiens" RELATED misspelling [] +synonym: "Homo spiens" RELATED misspelling [] +synonym: "human" EXACT genbank_common_name [] +synonym: "Humo sapiens" RELATED misspelling [] +synonym: "man" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9605 ! Homo +property_value: has_rank NCBITaxon:species +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: PATO:0000001 +name: quality +namespace: quality +alt_id: PATO:0000072 +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +synonym: "trait" EXACT [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000161 +name: rate +namespace: quality +def: "A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time." [PATOC:melissa] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002062 ! physical quality of a process +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001236 +name: process quality +namespace: quality +alt_id: PATO:0001239 +alt_id: PATO:0001240 +def: "A quality which inheres in an process." [PATOC:GVG] +comment: See comments of relational quality of a physical entity. +synonym: "quality of a process" EXACT [] +synonym: "quality of occurrent" EXACT [] +synonym: "quality of process" EXACT [] +synonym: "relational quality of occurrent" EXACT [] +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001241 +name: physical object quality +namespace: quality +alt_id: PATO:0001237 +alt_id: PATO:0001238 +def: "A quality which inheres in a continuant." [PATOC:GVG] +comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. +synonym: "monadic quality of a continuant" EXACT [] +synonym: "monadic quality of an object" NARROW [] +synonym: "monadic quality of continuant" NARROW [] +synonym: "multiply inhering quality of a physical entity" EXACT [] +synonym: "quality of a continuant" EXACT [] +synonym: "quality of a single physical entity" EXACT [] +synonym: "quality of an object" EXACT [] +synonym: "quality of continuant" EXACT [] +xref: snap:Quality +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001338 +name: mixed sex +namespace: quality +def: "A biological sex quality inhering in a population of multiple sexes." [MGED:MGED] +comment: For example a mixture of females and male or males and hermaphrodites. +subset: value_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001415 +name: morbidity +namespace: quality +def: "A quality inhering in a population by virtue of the proportion of its members that are ill at a given time." [PATOC:GVG] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002003 +name: population quality +namespace: quality +def: "A quality that inheres in an entire population or part of a population." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002062 +name: physical quality of a process +namespace: quality +subset: attribute_slim +is_a: PATO:0001236 ! process quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +created_by: george +creation_date: 2009-06-05T09:16:46Z + +[Term] +id: PCO:0000000 +name: collection of organisms +def: "A material entity that consists of two or more organisms, viruses, or viroids." [] +comment: May be of the same or different species. +is_a: BFO:0000027 ! object aggregate +is_a: PCO:0000031 ! organismal entity +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "group of organism" xsd:string +property_value: IAO:0000118 "organism collection" xsd:string + +[Term] +id: PCO:0000001 +name: population of organisms +def: "A collection of organisms, all of the same species, that live in the same place." [] +comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000112 "" xsd:string +property_value: IAO:0000112 "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 ISBN:0878932739 xsd:string + +[Term] +id: PCO:0000002 +name: ecological community +def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] +comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +property_value: IAO:0000118 "multispecies community" xsd:string +property_value: IAO:0000119 ISBN:0865423504 xsd:string + +[Term] +id: PCO:0000003 +name: quality of a population +def: "A quality that inheres in a biological population." [] +comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. +is_a: PATO:0002003 ! population quality +intersection_of: PATO:0002003 ! population quality +intersection_of: RO:0000052 PCO:0000001 ! population of organisms +relationship: RO:0000052 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000004 +name: quality of an ecological community +def: "A quality that inheres in a community." [] +comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. +is_a: PATO:0002003 ! population quality +intersection_of: PATO:0002003 ! population quality +intersection_of: RO:0000052 PCO:0000002 ! ecological community +relationship: RO:0000052 PCO:0000002 ! ecological community +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000005 +name: population process +def: "A process that has as primary participant a population. " [] +comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +is_a: BFO:0000015 ! process +relationship: RO:0000057 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000006 +name: population birth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000007 +name: population death rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000008 +name: population growth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string + +[Term] +id: PCO:0000009 +name: obsolete carrying capacity +def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] +is_a: ObsoleteClass +property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +property_value: IAO:0000119 ISBN:0878932739 xsd:string +property_value: IAO:0000231 IAO:0000423 +is_obsolete: true + +[Term] +id: PCO:0000010 +name: community species richness +def: "The number of different species represented in an ecological community." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string + +[Term] +id: PCO:0000011 +name: population growth +def: "A process that leads to a change in the number of individuals (positive or negative) in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000012 +name: logistic population growth +def: "A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000013 +name: exponential population growth +def: "A population growth process that leads to an exponential increase in the number of individuals in a population." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000014 +name: predator role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000015 +name: prey role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000016 +name: symbiont role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000017 +name: species as a collection of organisms +def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string + +[Term] +id: PCO:0000018 +name: single-species collection of organisms +def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000118 "collection of organisms of the same species" xsd:string + +[Term] +id: PCO:0000019 +name: community species diversity +def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] +comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string + +[Term] +id: PCO:0000020 +name: family +def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] +comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string +property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string + +[Term] +id: PCO:0000021 +name: population extinction +def: "A population process that ultimately leads to the death of all individuals in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000022 +name: species extinction +def: "A process that ultimately leads to the death of all individuals in a population." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000023 +name: community species evenness +def: "A quality of a community that reflects how close in abundance all species in a community are." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_evenness" xsd:string + +[Term] +id: PCO:0000024 +name: household +def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] +is_a: PCO:0000031 ! organismal entity +relationship: RO:0002321 ENVO:01000744 ! human dwelling +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! Homo sapiens +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string + +[Term] +id: PCO:0000025 +name: red population +comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000026 +name: red organism +comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000027 +name: collection of humans +def: "A collection of organisms of the same species that has as members only humans." [] +is_a: PCO:0000018 ! single-species collection of organisms +intersection_of: PCO:0000018 ! single-species collection of organisms +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! Homo sapiens +relationship: RO:0002351 NCBITaxon:9606 ! Homo sapiens +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "human community" xsd:string +property_value: IAO:0000118 "human population" xsd:string + +[Term] +id: PCO:0000028 +name: community +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). +is_a: ObsoleteClass +property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000029 +name: multi-species collection of organisms +def: "A collection of organisms that consists of two or more organisms from at least two species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string + +[Term] +id: PCO:0000030 +name: agricultural household +name: obsolete organismal entity +def: "A household in which the majority of the income of its members is derived from agricultural activities." [] +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: ObsoleteClass +is_a: PCO:0000024 ! household +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string +property_value: IAO:0000231 "wrong IRI form" xsd:string +is_obsolete: true +replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 + +[Term] +id: PCO:0000031 +name: organismal entity +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: BFO:0000040 ! material entity +union_of: CARO:0001010 ! organism or virus or viroid +union_of: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 + +[Term] +id: PCO:0000032 +name: biological family +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +is_a: PCO:0000020 ! family +property_value: IAO:0000118 "genealogical family" xsd:string +property_value: IAO:0000119 "Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/" xsd:string + +[Term] +id: PCO:0000033 +name: human social gathering activity +def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] +is_a: GO:0035176 ! social behavior +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000034 +name: human community event +def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000035 +name: party +def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000037 +name: potluck +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string +property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000038 +name: wedding +def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000039 +name: baby shower +def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000040 +name: tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: PCO:0000002 ! ecological community +relationship: BFO:0000050 ENVO:01001369 ! tidal mangrove shrubland +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string + +[Term] +id: PCO:0000041 +name: invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: PATO:0001241 ! physical object quality + +[Term] +id: PCO:0000042 +name: microbe +synonym: "microbial organism" EXACT [] +is_a: CARO:0001010 ! organism or virus or viroid +relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye + +[Term] +id: PCO:0000043 +name: collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe +intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000044 +name: multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: PCO:0000029 ! multi-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000045 +name: single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000046 +name: microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: PCO:0000001 ! population of organisms +is_a: PCO:0000045 ! single species collection of microbes +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0001000 +name: pair of interacting organisms +def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] +is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid + +[Term] +id: PCO:0001001 +name: pair of interacting organisms of the same species +is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0001000 ! pair of interacting organisms + +[Term] +id: PCO:1000000 +name: migratory population +def: "A population which is participating in a migration process." [] +is_a: PCO:0000001 ! population of organisms +relationship: RO:0000056 PCO:1000001 ! population migration +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:1000001 +name: population migration +def: "A population process during which a population moves from one area to another." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Migration xsd:string + +[Term] +id: PCO:1000002 +name: human population migration +def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration +is_a: PCO:1000001 ! population migration +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000003 +name: human migratory population +def: "A migratory population of humans, travelling with the intention of settling in a new area." [] +is_a: PCO:0000027 ! collection of humans +relationship: RO:0000056 PCO:1000002 ! human population migration +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000004 +name: microbial community +def: "An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness." [] +comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. +synonym: "microbiota" BROAD [] +is_a: PCO:0000002 ! ecological community +is_a: PCO:0000044 ! multi-species collection of microbes +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string +property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Synonym +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: SynonymType +is_a: IAO:0000102 ! data about an ontology part + diff --git a/pco-full.owl b/pco-full.owl new file mode 100644 index 0000000..c95c12c --- /dev/null +++ b/pco-full.owl @@ -0,0 +1,4991 @@ + + + + + http://orcid.org/0000-0002-4366-3088 + https://orcid.org/0000-0001-8815-0078 + David Osumi-Sutherland + Jie Zheng + Pier Luigi Buttigieg + Ramona Walls + http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + editor preferred term + + + + + + + + example + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + editor note + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + alternative term + + + + + + + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + + + + + is denotator type + relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from + + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + + + + + + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + + has associated axiom(fol) + + + + + + + + is allocated id range + Add as annotation triples in the granting ontology + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + is allocated id range + + + + + + + + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + 2018-09-21T16:43:39Z + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + + has axiom label + + + + + + + + term replaced by + + Add as annotation triples in the granting ontology + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + term replaced by + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_alternative_id + + + + + + + + + + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + + + + + + + + + + has_obo_namespace + + + + + + + + + has_related_synonym + + + + + + + + + + + + + + + + + + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + continuant + Continuant + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + + + + + occurrent + Occurrent + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + + + + + + + + + object-aggregate + ObjectAggregate + a collection of cells in a blood biobank. + a swarm of bees is an aggregate of members who are linked together through natural bonds + a symphony orchestra + an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) + defined by fiat: the aggregate of members of an organization + defined through physical attachment: the aggregate of atoms in a lump of granite + defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container + defined via attributive delimitations such as: the patients in this hospital + the aggregate of bearings in a constant velocity axle joint + the aggregate of blood cells in your body + the nitrogen atoms in the atmosphere + the restaurants in Palo Alto + your collection of Meissen ceramic plates. + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + object aggregate + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + + + + + + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + + + + + + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + + + + + + + + + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + site + + + + + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + + + + + + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + + + + + immaterial + ImmaterialEntity + BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 + + immaterial entity + + + + + + + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + organism or virus + Melissa Haendel + 9/18/11 + organism or virus or viroid + + + + + + + + + An individual member of a clade. + organism + mah + 7.16.2011 + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + organism + + + + + + + + + A feature that has been constructed by deliberate human effort. + "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference + constructed feature + construction + + + + + A feature that has been constructed by deliberate human effort. + MA:ma + + + + + + + + + A material entity which determines an environmental system. + ENVO + ENVO:00002297 + A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. + environmental feature + + + + + A material entity which determines an environmental system. + DOI:10.1186/2041-1480-4-43 + NM:nm + ORCID:0000-0002-4366-3088 + + + + + + + + + A system which has the disposition to environ one or more material entities. + 2013-09-23T16:04:08Z + EcoLexicon:environment + environment + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + + A system which has the disposition to environ one or more material entities. + DOI:10.1186/2041-1480-4-43 + + + + + + + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. + Subclasses will be added by inference. + human dwelling + + + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 + + + + + + + + + A material part of an astronomical body. + envoAstro + envoPolar + astronomical body part + + + + + + + + + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. + http://orcid.org/0000-0002-4366-3088 + CMECS:577 + https://cmecscatalog.org/cmecs/classification/unit/577.html + envoCmecs + envoMarine + This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" + tidal mangrove shrubland + + + + + + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + janelomax + 2012-09-20T14:06:08Z + GO:0044708 + Wikipedia:Behavior + behavioral response to stimulus + behaviour + behavioural response to stimulus + biological_process + single-organism behavior + GO:0007610 + + + + 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. +2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). + + behavior + + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + GOC:ems + GOC:jl + ISBN:0395448956 + PMID:20160973 + + + + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + janelomax + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + + biological_process + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + + Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + Wikipedia:Social_behavior + social behaviour + biological_process + cooperative behavior + GO:0035176 + Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. + + social behavior + + + + + Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + GOC:jh2 + PMID:12848939 + Wikipedia:Social_behavior + + + + + + + + + Any process in which an organism has an effect on an organism of a different species. + interaction with another species + interspecies interaction + interspecies interaction with other organisms + biological_process + GO:0044419 + + + + interspecies interaction between organisms + + + + + Any process in which an organism has an effect on an organism of a different species. + GOC:cc + + + + + + + + + Any process in which an organism has an effect on an organism of the same species. + intraspecies interaction with other organisms + biological_process + GO:0051703 + + + intraspecies interaction between organisms + + + + + Any process in which an organism has an effect on an organism of the same species. + GOC:ai + + + + + + + + + + A biological process which involves another organism of the same or different species. + GO:0051706 + interaction between organisms + physiological interaction between organisms + physiological interaction with other organism + biological_process + GO:0051704 + + + + multi-organism process + + + + + A biological process which involves another organism of the same or different species. + GOC:jl + + + + + + + + + + Any process in which an organism has a behavioral effect on another organism of the same or different species. + GO:0023032 + GO:0044709 + behavioral interaction between organisms + behavioral interaction with other organism + behavioural interaction between organisms + behavioural interaction with other organism + behavioral signaling + behavioral signalling + biological_process + GO:0051705 + + + multi-organism behavior + + + + + Any process in which an organism has a behavioral effect on another organism of the same or different species. + GOC:ai + + + + + behavioral signalling + GOC:mah + + + + + + + + + data item + + + + + + + + + information content entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + cjm + 2018-05-20T20:55:03Z + ontology module + + + + + + + + + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + cjm + 2018-05-20T20:55:30Z + base ontology module + + + + + + + + + + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + cjm + 2018-05-20T20:55:47Z + editors ontology module + + + + + + + + + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + cjm + 2018-05-20T20:56:13Z + main release ontology module + + + + + + + + + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + cjm + 2018-05-20T20:56:23Z + bridge ontology module + + + + + + + + + + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + cjm + 2018-05-20T20:56:47Z + import ontology module + + + + + + + + + + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + cjm + 2018-05-20T20:58:11Z + subset ontology module + + + + + + + + + + + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + cjm + 2018-05-20T20:58:38Z + curation subset ontology module + + + + + + + + + An ontology module that is intended for usage in analysis or discovery applications. + cjm + 2018-05-20T20:58:49Z + analysis subset ontology module + + + + + + + + + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + cjm + 2018-05-20T20:59:19Z + single layer subset ontology module + + + + + + + + + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + cjm + 2018-05-20T20:59:57Z + exclusion subset ontology module + + + + + + + + + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + cjm + 2018-05-20T21:00:14Z + external import ontology module + + + + + + + + + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + cjm + 2018-05-20T21:14:16Z + species subset ontology module + + + + + + + + + + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + cjm + 2018-05-20T21:20:33Z + reasoned ontology module + + + + + + + + + + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + cjm + 2018-05-20T21:21:12Z + generated ontology module + + + + + + + + + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + cjm + 2018-05-20T21:21:21Z + template generated ontology module + + + + + + + + + + + + cjm + 2018-05-20T21:28:15Z + taxonomic bridge ontology module + + + + + + + + + cjm + 2018-05-22T04:15:54Z + ontology module subsetted by expressivity + + + + + + + + + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + cjm + 2018-05-22T04:16:10Z + obo basic subset ontology module + + + + + + + + + + cjm + 2018-05-22T04:16:28Z + ontology module subsetted by OWL profile + + + + + + + + + cjm + 2018-05-22T04:16:48Z + EL++ ontology module + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Vira + Viridae + viruses + + Viruses + + + + + Vira + + + + + + Viridae + + + + + + viruses + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Teleostomi + + + + + + + + + NCBITaxon:40673 + GC_ID:1 + bony vertebrates + ncbi_taxonomy + + Euteleostomi + + + + + bony vertebrates + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Viroid + viroids + + Viroids + + + + + Viroid + + + + + + viroids + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Charophyta/Embryophyta group + charophyte/embryophyte group + + Streptophytina + + + + + Charophyta/Embryophyta group + + + + + + charophyte/embryophyte group + + + + + + + + + GC_ID:1 + ncbi_taxonomy + biota + + cellular organisms + + + + + biota + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Dipnotetrapodomorpha + + + + + + + + + GC_ID:1 + PMID:11743200 + PMID:11791233 + ncbi_taxonomy + Boreotheria + + Boreoeutheria + + + + + Boreotheria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Acrogymnospermae + + + + + + + + + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11542017 + PMID:11542087 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:270744 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 + eubacteria + ncbi_taxonomy + Monera + Procaryotae + Prokaryota + Prokaryotae + bacteria + prokaryote + prokaryotes + + Bacteria + + + + + prokaryotes + + + + + + eubacteria + + + + + + Monera + + + + + + Procaryotae + + + + + + Prokaryota + + + + + + Prokaryotae + + + + + + bacteria + + + + + + prokaryote + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Homo/Pan/Gorilla group + + Homininae + + + + + Homo/Pan/Gorilla group + + + + + + + + + + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11541975 + PMID:11542064 + PMID:11542149 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:25527841 + PMID:270744 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 + ncbi_taxonomy + Archaebacteria + Mendosicutes + Metabacteria + Monera + Procaryotae + Prokaryota + Prokaryotae + archaea + prokaryote + prokaryotes + + Archaea + + + + + Archaebacteria + + + + + + Mendosicutes + + + + + + Metabacteria + + + + + + Monera + + + + + + Procaryotae + + + + + + Prokaryota + + + + + + Prokaryotae + + + + + + archaea + + + + + + prokaryote + + + + + + prokaryotes + + + + + + + + + + + GC_ID:1 + PMID:23020233 + eucaryotes + eukaryotes + ncbi_taxonomy + Eucarya + Eucaryotae + Eukarya + Eukaryotae + eukaryotes + + Eukaryota + + + + + eucaryotes + + + + + + eukaryotes + + + + + + Eucarya + + + + + + Eucaryotae + + + + + + Eukarya + + + + + + Eukaryotae + + + + + + eukaryotes + + + + + + + + + + + GC_ID:1 + PMID:23020233 + green algae + ncbi_taxonomy + Chlorophycota + Chlorophyta sensu Bremer 1985 + algae + green algae + + Chlorophyta + + + + + green algae + + + + + + Chlorophycota + + + + + + Chlorophyta sensu Bremer 1985 + + + + + + algae + + + + + + green algae + + + + + + + + + + + GC_ID:1 + PMID:11214319 + PMID:12082125 + PMID:12878460 + PMID:15522813 + ncbi_taxonomy + + Euarchontoglires + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Anthropoidea + + Simiiformes + + + + + Anthropoidea + + + + + + + + + + + GC_ID:1 + ape + apes + ncbi_taxonomy + + Hominoidea + + + + + ape + + + + + + apes + + + + + + + + + + GC_ID:1 + higher plants + land plants + plants + ncbi_taxonomy + land plants + + Embryophyta + + + + + higher plants + + + + + + land plants + + + + + + plants + + + + + + land plants + + + + + + + + + + GC_ID:1 + tetrapods + ncbi_taxonomy + + Tetrapoda + + + + + tetrapods + + + + + + + + + + GC_ID:1 + amniotes + ncbi_taxonomy + + Amniota + + + + + amniotes + + + + + + + + + + GC_ID:1 + Theria + ncbi_taxonomy + + Theria <Mammalia> + + + + + Theria + + + + + + + + + + + GC_ID:1 + green plants + ncbi_taxonomy + Chlorobionta + Chlorophyta/Embryophyta group + chlorophyte/embryophyte group + green plants + + Viridiplantae + + + + + green plants + + + + + + Chlorobionta + + + + + + Chlorophyta/Embryophyta group + + + + + + chlorophyte/embryophyte group + + + + + + green plants + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Fungi/Metazoa group + opisthokonts + + Opisthokonta + + + + + Fungi/Metazoa group + + + + + + opisthokonts + + + + + + + + + + + GC_ID:1 + metazoans + multicellular animals + ncbi_taxonomy + Animalia + animals + + Metazoa + + + + + metazoans + + + + + + multicellular animals + + + + + + Animalia + + + + + + animals + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Bilateria + + + + + + + + + GC_ID:1 + deuterostomes + ncbi_taxonomy + + Deuterostomia + + + + + deuterostomes + + + + + + + + + + GC_ID:1 + PMID:25249442 + angiosperms + flowering plants + ncbi_taxonomy + Angiospermae + flowering plants + + Magnoliophyta + + + + + angiosperms + + + + + + flowering plants + + + + + + Angiospermae + + + + + + flowering plants + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Streptophyta + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Haplorrhini + + + + + + + + + + GC_ID:1 + mammals + ncbi_taxonomy + mammals + + Mammalia + + + + + mammals + + + + + + mammals + + + + + + + + + + GC_ID:1 + vascular plants + ncbi_taxonomy + vascular plants + + Tracheophyta + + + + + vascular plants + + + + + + vascular plants + + + + + + + + + + GC_ID:1 + seed plants + ncbi_taxonomy + seed plants + + Spermatophyta + + + + + seed plants + + + + + + seed plants + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Eumetazoa + + + + + + + + + + GC_ID:1 + chordates + ncbi_taxonomy + chordates + + Chordata + + + + + chordates + + + + + + chordates + + + + + + + + + + GC_ID:1 + Vertebrata + vertebrates + ncbi_taxonomy + vertebrates + + Vertebrata <Metazoa> + + + + + Vertebrata + + + + + + vertebrates + + + + + + vertebrates + + + + + + + + + + GC_ID:1 + Gnathostomata + jawed vertebrates + ncbi_taxonomy + + Gnathostomata <vertebrate> + + + + + Gnathostomata + + + + + + jawed vertebrates + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + euphyllophytes + + Euphyllophyta + + + + + euphyllophytes + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Sarcopterygii + + + + + + + + + + GC_ID:1 + Craniata + ncbi_taxonomy + + Craniata <chordata> + + + + + Craniata + + + + + + + + + + GC_ID:1 + eutherian mammals + placental mammals + placentals + ncbi_taxonomy + Placentalia + placentals + + Eutheria + + + + + eutherian mammals + + + + + + placental mammals + + + + + + placentals + + + + + + Placentalia + + + + + + placentals + + + + + + + + + + + GC_ID:1 + primate + ncbi_taxonomy + Primata + primates + + Primates + + + + + primate + + + + + + Primata + + + + + + primates + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Catarrhini + + + + + + + + + + GC_ID:1 + great apes + ncbi_taxonomy + Pongidae + + Hominidae + + + + + great apes + + + + + + Pongidae + + + + + + + + + + + GC_ID:1 + humans + ncbi_taxonomy + + Homo + + + + + humans + + + + + + + + + + + GC_ID:1 + human + man + ncbi_taxonomy + Home sapiens + Homo sampiens + Homo sapeins + Homo sapian + Homo sapians + Homo sapien + Homo sapience + Homo sapiense + Homo sapients + Homo sapines + Homo spaiens + Homo spiens + Humo sapiens + + Homo sapiens + + + + + human + + + + + + man + + + + + + Home sapiens + + + + + + Homo sampiens + + + + + + Homo sapeins + + + + + + Homo sapian + + + + + + Homo sapians + + + + + + Homo sapien + + + + + + Homo sapience + + + + + + Homo sapiense + + + + + + Homo sapients + + + + + + Homo sapines + + + + + + Homo spaiens + + + + + + Homo spiens + + + + + + Humo sapiens + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATO:0000072 + trait + quality + PATO:0000001 + + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + + rate + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + PATOC:melissa + + + + + + + + + A quality which inheres in an process. + PATO:0001239 + PATO:0001240 + quality of a process + quality of occurrent + quality of process + relational quality of occurrent + quality + PATO:0001236 + See comments of relational quality of a physical entity. + + process quality + + + + + A quality which inheres in an process. + PATOC:GVG + + + + + + + + + A quality which inheres in a continuant. + PATO:0001237 + PATO:0001238 + snap:Quality + monadic quality of a continuant + multiply inhering quality of a physical entity + quality of a continuant + quality of a single physical entity + quality of an object + quality of continuant + monadic quality of an object + monadic quality of continuant + quality + PATO:0001241 + Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. + + physical object quality + + + + + A quality which inheres in a continuant. + PATOC:GVG + + + + + + + + + A biological sex quality inhering in a population of multiple sexes. + quality + PATO:0001338 + + For example a mixture of females and male or males and hermaphrodites. + + mixed sex + + + + + A biological sex quality inhering in a population of multiple sexes. + MGED:MGED + + + + + + + + + A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. + quality + PATO:0001415 + + + + morbidity + + + + + A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. + PATOC:GVG + + + + + + + + + A quality that inheres in an entire population or part of a population. + quality + PATO:0002003 + + + population quality + + + + + A quality that inheres in an entire population or part of a population. + PATOC:GVG + + + + + + + + + george + 2009-06-05T09:16:46Z + quality + PATO:0002062 + + + physical quality of a process + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. + + A material entity that consists of two or more organisms, viruses, or viroids. + group of organism + organism collection + May be of the same or different species. + collection of organisms + + + + + + + + + + This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed. + + A collection of organisms, all of the same species, that live in the same place. + ISBN:0878932739 + It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. + +Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. + population of organisms + + + + + + + + + + + + + + 2 + + + + + + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. + multispecies community + ISBN:0865423504 + Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. + ecological community + + + + + + + + + + + + + + + + + + + + + + + + + + + A quality that inheres in a biological population. + See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. + quality of a population + + + + + + + + + + + + + + + + + + + + + + + + + + + A quality that inheres in a community. + These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. + quality of an ecological community + + + + + + + + + + + + + + + + A process that has as primary participant a population. + Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + population process + + + + + + + + + + population birth rate + + + + + + + + + + population death rate + + + + + + + + + + Is a rate a quality? Population growth rate may be better classified as a process profile. + population growth rate + + + + + + + + + The maximum number of individuals that can be supported in a population that is growing according to logistic growth. + Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE. + ISBN:0878932739 + + obsolete carrying capacity + true + + + + + + + + + + The number of different species represented in an ecological community. + This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019). + adapted from http://en.wikipedia.org/wiki/Species_richness + community species richness + + + + + + + + + + A process that leads to a change in the number of individuals (positive or negative) in a population. + population growth + + + + + + + + + + A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat. + logistic population growth + + + + + + + + + + A population growth process that leads to an exponential increase in the number of individuals in a population. + exponential population growth + + + + + + + + + + predator role + + + + + + + + + + prey role + + + + + + + + + + symbiont role + + + + + + + + + + A collection of organisms that has as parts every organism of given species and no organisms of any other species. + At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. + species as a collection of organisms + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + + A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. + collection of organisms of the same species + single-species collection of organisms + + + + + + + + + + The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness. + If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity. + adapted from http://en.wikipedia.org/wiki/Species_diversity + The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. + community species diversity + + + + + + + + + + A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. + Needs axioms for family relationships. + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 + Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. + family + + + + + + + + + + A population process that ultimately leads to the death of all individuals in a population. + population extinction + + + + + + + + + + A process that ultimately leads to the death of all individuals in a population. + species extinction + + + + + + + + + If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. + + A quality of a community that reflects how close in abundance all species in a community are. + adapted from http://en.wikipedia.org/wiki/Species_evenness + community species evenness + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. + Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household + household + + + + + + + + + + This is an example population added to demonstrate the modeling pattern for collections of organisms. + red population + true + + + + + + + + + + An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. + red organism + true + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + A collection of organisms of the same species that has as members only humans. + human community + human population + collection of humans + + + + + + + + + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. + Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. + + These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). + community + true + + + + + + + + + + A collection of organisms that consists of two or more organisms from at least two species. + Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". + + multi-species collection of organisms + + + + + + + + + + A household in which the majority of the income of its members is derived from agricultural activities. + This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term. + agricultural household + + + + + + + + + + + + + + + + + + A material entity that is one or more organisms, viruses or viroids. + organismal entity + + + + + + + + + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. + genealogical family + Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/ + biological family + + + + + + + + + + + + + + + A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. + Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029 + GenEpiO curators + human social gathering activity + + + + + + + + + A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034 + GenEpio curators + human community event + + + + + + + + + A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030 + GenEpiO curators + party + + + + + + + + + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. + GenEpio curators + potluck + + + + + + + + + A human social gathering at which two people are married. May include a legal or social ceremony. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 + GenEpio curators + wedding + + + + + + + + + A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 + GenEpiO curators + baby shower + + + + + + + + + + + + + + + + + + 2 + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + pair of interacting organisms of the same species + + + + + + + + + + + + + + + + A population which is participating in a migration process. + migratory population + + + + + + + + + + A population process during which a population moves from one area to another. + https://en.wikipedia.org/wiki/Migration + The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. + population migration + + + + + + + + + + + + + + + + A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location. + https://en.wikipedia.org/wiki/Human_migration + The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration + human population migration + + + + + + + + + + + + + + + + A migratory population of humans, travelling with the intention of settling in a new area. + https://en.wikipedia.org/wiki/Human_migration + human migratory population + + + + + + + + + + + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. + A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 + http://orcid.org/0000-0002-4366-3088 + http://dx.doi.org/10.1038/ismej.2009.88 + microbiota + The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. + microbial community + + + + + + + + + A material entity that is one or more organisms, viruses or viroids. + wrong IRI form + http://purl.obolibrary.org/obo/PCO_0000031 + obsolete organismal entity + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community + + + + + + + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + + + + + + + microbial organism + microbe + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/pco.obo b/pco.obo new file mode 100644 index 0000000..f15f70f --- /dev/null +++ b/pco.obo @@ -0,0 +1,1820 @@ +format-version: 1.2 +data-version: releases/2020-02-13 +remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. +ontology: pco +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string +property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: BFO:0000179 "continuant" xsd:string +property_value: BFO:0000180 "Continuant" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: BFO:0000179 "occurrent" xsd:string +property_value: BFO:0000180 "Occurrent" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "ic" xsd:string +property_value: BFO:0000180 "IndependentContinuant" xsd:string +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +is_a: BFO:0000003 ! occurrent +property_value: BFO:0000179 "process" xsd:string +property_value: BFO:0000180 "Process" xsd:string +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +is_a: BFO:0000020 ! specifically dependent continuant +property_value: BFO:0000179 "realizable" xsd:string +property_value: BFO:0000180 "RealizableEntity" xsd:string +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "sdc" xsd:string +property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +is_a: BFO:0000017 ! realizable entity +property_value: BFO:0000179 "role" xsd:string +property_value: BFO:0000180 "Role" xsd:string +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000027 +name: object aggregate +is_a: BFO:0000040 ! material entity +property_value: BFO:0000179 "object-aggregate" xsd:string +property_value: BFO:0000180 "ObjectAggregate" xsd:string +property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string +property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string +property_value: IAO:0000112 "a symphony orchestra" xsd:string +property_value: IAO:0000112 "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)" xsd:string +property_value: IAO:0000112 "defined by fiat: the aggregate of members of an organization" xsd:string +property_value: IAO:0000112 "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string +property_value: IAO:0000112 "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string +property_value: IAO:0000112 "defined via attributive delimitations such as: the patients in this hospital" xsd:string +property_value: IAO:0000112 "the aggregate of bearings in a constant velocity axle joint" xsd:string +property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:string +property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string +property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string +property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string +property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} +property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000029 +name: site +is_a: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "site" xsd:string +property_value: BFO:0000180 "Site" xsd:string +property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string +property_value: IAO:0000112 "a rabbit hole" xsd:string +property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string +property_value: IAO:0000112 "Manhattan Canyon)" xsd:string +property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string +property_value: IAO:0000112 "the Grand Canyon" xsd:string +property_value: IAO:0000112 "the hold of a ship" xsd:string +property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string +property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string +property_value: IAO:0000112 "the interior of your bedroom" xsd:string +property_value: IAO:0000112 "the interior of your office" xsd:string +property_value: IAO:0000112 "the interior of your refrigerator" xsd:string +property_value: IAO:0000112 "the lumen of your gut" xsd:string +property_value: IAO:0000112 "the Piazza San Marco" xsd:string +property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string +property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +is_a: BFO:0000002 ! continuant +property_value: BFO:0000179 "gdc" xsd:string +property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "material" xsd:string +property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant +property_value: BFO:0000179 "immaterial" xsd:string +property_value: BFO:0000180 "ImmaterialEntity" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: CARO:0001010 +name: organism or virus or viroid +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +is_a: PCO:0000031 ! organismal entity +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "organism or virus" xsd:string + +[Term] +id: CARO:0010004 +name: organism +def: "An individual member of a clade." [] +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +is_a: CARO:0001010 ! organism or virus or viroid +property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string +property_value: IAO:0000589 "organism" xsd:string + +[Term] +id: DbXref +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Definition +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: ENVO:00000070 +name: construction +def: "A feature that has been constructed by deliberate human effort." [MA:ma] +synonym: "constructed feature" EXACT [] +is_a: ENVO:01000813 ! astronomical body part +property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string + +[Term] +id: ENVO:00002297 +name: environmental feature +namespace: ENVO +def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] +comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. +is_a: BFO:0000040 ! material entity + +[Term] +id: ENVO:01000254 +name: environmental system +def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +synonym: "environment" EXACT [] +xref: EcoLexicon:environment +is_a: BFO:0000040 ! material entity +creation_date: 2013-09-23T16:04:08Z + +[Term] +id: ENVO:01000744 +name: human dwelling +def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] +is_a: ENVO:00000070 ! construction +property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string + +[Term] +id: ENVO:01000813 +name: astronomical body part +def: "A material part of an astronomical body." [] +subset: envoAstro +subset: envoPolar +is_a: ENVO:00002297 ! environmental feature + +[Term] +id: ENVO:01001369 +name: tidal mangrove shrubland +alt_id: CMECS:577 +def: "A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas." [] +comment: This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" +subset: envoCmecs +subset: envoMarine +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ENVO:01000254 ! environmental system +created_by: http://orcid.org/0000-0002-4366-3088 + +[Term] +id: GO:0007610 +name: behavior +namespace: biological_process +alt_id: GO:0044708 +def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] +comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). +subset: gocheck_do_not_manually_annotate +subset: goslim_agr +subset: goslim_flybase_ribbon +synonym: "behavioral response to stimulus" EXACT [] +synonym: "behaviour" EXACT [] +synonym: "behavioural response to stimulus" EXACT [] +synonym: "single-organism behavior" RELATED [] +xref: Wikipedia:Behavior +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-20T14:06:08Z + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0035176 +name: social behavior +namespace: biological_process +def: "Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group." [GOC:jh2, PMID:12848939, Wikipedia:Social_behavior] +comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. +synonym: "cooperative behavior" RELATED [] +synonym: "social behaviour" EXACT [] +xref: Wikipedia:Social_behavior +is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051705 ! multi-organism behavior +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0044419 +name: interspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +subset: goslim_candida +subset: goslim_pir +synonym: "interaction with another species" EXACT [] +synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051703 +name: intraspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: goslim_pir +synonym: "intraspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051704 +name: multi-organism process +namespace: biological_process +alt_id: GO:0051706 +def: "A biological process which involves another organism of the same or different species." [GOC:jl] +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "interaction between organisms" EXACT [] +synonym: "physiological interaction between organisms" EXACT [] +synonym: "physiological interaction with other organism" EXACT [] +is_a: BFO:0000015 ! process +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051705 +name: multi-organism behavior +namespace: biological_process +alt_id: GO:0023032 +alt_id: GO:0044709 +def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] +subset: goslim_pir +synonym: "behavioral interaction between organisms" EXACT [] +synonym: "behavioral interaction with other organism" EXACT [] +synonym: "behavioral signaling" NARROW [] +synonym: "behavioral signalling" NARROW [GOC:mah] +synonym: "behavioural interaction between organisms" EXACT [] +synonym: "behavioural interaction with other organism" EXACT [] +is_a: GO:0007610 ! behavior +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: IAO:0000027 +name: data item +is_a: IAO:0000030 ! information content entity + +[Term] +id: IAO:0000030 +name: information content entity +is_a: BFO:0000031 ! generically dependent continuant + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:03Z + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 +created_by: cjm +creation_date: 2018-05-20T20:55:30Z + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "source ontology module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:47Z + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:56:13Z + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies +created_by: cjm +creation_date: 2018-05-20T20:56:23Z + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract +created_by: cjm +creation_date: 2018-05-20T20:56:47Z + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide +created_by: cjm +creation_date: 2018-05-20T20:58:11Z + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:38Z + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:49Z + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "ribbon subset" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:19Z + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "antislim" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:57Z + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000118 "external import" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:00:14Z + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +created_by: cjm +creation_date: 2018-05-20T21:14:16Z + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso http://robot.obolibrary.org/reason +created_by: cjm +creation_date: 2018-05-20T21:20:33Z + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:21:12Z + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ +created_by: cjm +creation_date: 2018-05-20T21:21:21Z + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +created_by: cjm +creation_date: 2018-05-20T21:28:15Z + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-22T04:15:54Z + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: seeAlso "6.2" +created_by: cjm +creation_date: 2018-05-22T04:16:10Z + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +created_by: cjm +creation_date: 2018-05-22T04:16:28Z + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +created_by: cjm +creation_date: 2018-05-22T04:16:48Z + +[Term] +id: NCBITaxon:10239 +name: Viruses +namespace: ncbi_taxonomy +synonym: "Vira" RELATED synonym [] +synonym: "Viridae" RELATED synonym [] +synonym: "viruses" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117570 +name: Teleostomi +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:7776 ! Gnathostomata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117571 +name: Euteleostomi +namespace: ncbi_taxonomy +alt_id: NCBITaxon:40673 +synonym: "bony vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:117570 ! Teleostomi +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:12884 +name: Viroids +namespace: ncbi_taxonomy +synonym: "Viroid" RELATED synonym [] +synonym: "viroids" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131221 +name: Streptophytina +namespace: ncbi_taxonomy +synonym: "Charophyta/Embryophyta group" RELATED synonym [] +synonym: "charophyte/embryophyte group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:35493 ! Streptophyta +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131567 +name: cellular organisms +namespace: ncbi_taxonomy +synonym: "biota" RELATED synonym [] +xref: GC_ID:1 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1338369 +name: Dipnotetrapodomorpha +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:8287 ! Sarcopterygii +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437010 +name: Boreoeutheria +namespace: ncbi_taxonomy +synonym: "Boreotheria" RELATED synonym [] +xref: GC_ID:1 +xref: PMID:11743200 +xref: PMID:11791233 +is_a: NCBITaxon:9347 ! Eutheria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437180 +name: Acrogymnospermae +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2 +name: Bacteria +namespace: ncbi_taxonomy +synonym: "bacteria" RELATED blast_name [] +synonym: "eubacteria" EXACT genbank_common_name [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11542017 +xref: PMID:11542087 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:207598 +name: Homininae +namespace: ncbi_taxonomy +synonym: "Homo/Pan/Gorilla group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:9604 ! Hominidae +property_value: has_rank NCBITaxon:subfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2157 +name: Archaea +namespace: ncbi_taxonomy +synonym: "archaea" RELATED blast_name [] +synonym: "Archaebacteria" RELATED synonym [] +synonym: "Mendosicutes" RELATED synonym [] +synonym: "Metabacteria" RELATED synonym [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11541975 +xref: PMID:11542064 +xref: PMID:11542149 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:25527841 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2759 +name: Eukaryota +namespace: ncbi_taxonomy +synonym: "Eucarya" RELATED synonym [] +synonym: "Eucaryotae" RELATED synonym [] +synonym: "eucaryotes" EXACT genbank_common_name [] +synonym: "Eukarya" RELATED synonym [] +synonym: "Eukaryotae" RELATED synonym [] +synonym: "eukaryotes" EXACT common_name [] +synonym: "eukaryotes" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3041 +name: Chlorophyta +namespace: ncbi_taxonomy +synonym: "algae" RELATED in_part [] +synonym: "Chlorophycota" RELATED synonym [] +synonym: "Chlorophyta sensu Bremer 1985" RELATED synonym [] +synonym: "green algae" EXACT genbank_common_name [] +synonym: "green algae" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314146 +name: Euarchontoglires +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:11214319 +xref: PMID:12082125 +xref: PMID:12878460 +xref: PMID:15522813 +is_a: NCBITaxon:1437010 ! Boreoeutheria +property_value: has_rank NCBITaxon:superorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314293 +name: Simiiformes +namespace: ncbi_taxonomy +synonym: "Anthropoidea" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:376913 ! Haplorrhini +property_value: has_rank NCBITaxon:infraorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314295 +name: Hominoidea +namespace: ncbi_taxonomy +synonym: "ape" EXACT common_name [] +synonym: "apes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9526 ! Catarrhini +property_value: has_rank NCBITaxon:superfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3193 +name: Embryophyta +namespace: ncbi_taxonomy +synonym: "higher plants" EXACT common_name [] +synonym: "land plants" EXACT common_name [] +synonym: "land plants" RELATED blast_name [] +synonym: "plants" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:131221 ! Streptophytina +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32523 +name: Tetrapoda +namespace: ncbi_taxonomy +synonym: "tetrapods" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32524 +name: Amniota +namespace: ncbi_taxonomy +synonym: "amniotes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32523 ! Tetrapoda +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32525 +name: Theria +namespace: ncbi_taxonomy +synonym: "Theria" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:40674 ! Mammalia +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33090 +name: Viridiplantae +namespace: ncbi_taxonomy +synonym: "Chlorobionta" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] +synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "green plants" EXACT common_name [] +synonym: "green plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33154 +name: Opisthokonta +namespace: ncbi_taxonomy +synonym: "Fungi/Metazoa group" RELATED synonym [] +synonym: "opisthokonts" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33208 +name: Metazoa +namespace: ncbi_taxonomy +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33213 +name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:6072 ! Eumetazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33511 +name: Deuterostomia +namespace: ncbi_taxonomy +synonym: "deuterostomes" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33213 ! Bilateria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3398 +name: Magnoliophyta +namespace: ncbi_taxonomy +synonym: "Angiospermae" RELATED synonym [] +synonym: "angiosperms" EXACT common_name [] +synonym: "flowering plants" EXACT genbank_common_name [] +synonym: "flowering plants" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:25249442 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:35493 +name: Streptophyta +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:376913 +name: Haplorrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:9443 ! Primates +property_value: has_rank NCBITaxon:suborder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:40674 +name: Mammalia +namespace: ncbi_taxonomy +synonym: "mammals" EXACT genbank_common_name [] +synonym: "mammals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32524 ! Amniota +property_value: has_rank NCBITaxon:class +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58023 +name: Tracheophyta +namespace: ncbi_taxonomy +synonym: "vascular plants" EXACT common_name [] +synonym: "vascular plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:3193 ! Embryophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58024 +name: Spermatophyta +namespace: ncbi_taxonomy +synonym: "seed plants" EXACT common_name [] +synonym: "seed plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:78536 ! Euphyllophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33208 ! Metazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7711 +name: Chordata +namespace: ncbi_taxonomy +synonym: "chordates" EXACT genbank_common_name [] +synonym: "chordates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33511 ! Deuterostomia +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7742 +name: Vertebrata +namespace: ncbi_taxonomy +synonym: "Vertebrata" EXACT scientific_name [] +synonym: "vertebrates" EXACT genbank_common_name [] +synonym: "vertebrates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:89593 ! Craniata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7776 +name: Gnathostomata +namespace: ncbi_taxonomy +synonym: "Gnathostomata" EXACT scientific_name [] +synonym: "jawed vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7742 ! Vertebrata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:78536 +name: Euphyllophyta +namespace: ncbi_taxonomy +synonym: "euphyllophytes" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:58023 ! Tracheophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:8287 +name: Sarcopterygii +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:117571 ! Euteleostomi +property_value: has_rank NCBITaxon:superclass +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:89593 +name: Craniata +namespace: ncbi_taxonomy +synonym: "Craniata" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7711 ! Chordata +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9347 +name: Eutheria +namespace: ncbi_taxonomy +synonym: "eutherian mammals" EXACT common_name [] +synonym: "placental mammals" EXACT common_name [] +synonym: "Placentalia" RELATED synonym [] +synonym: "placentals" EXACT genbank_common_name [] +synonym: "placentals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32525 ! Theria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9443 +name: Primates +namespace: ncbi_taxonomy +synonym: "Primata" RELATED synonym [] +synonym: "primate" EXACT equivalent_name [] +synonym: "primates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:314146 ! Euarchontoglires +property_value: has_rank NCBITaxon:order +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9526 +name: Catarrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:314293 ! Simiiformes +property_value: has_rank NCBITaxon:parvorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9604 +name: Hominidae +namespace: ncbi_taxonomy +synonym: "great apes" EXACT genbank_common_name [] +synonym: "Pongidae" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:314295 ! Hominoidea +property_value: has_rank NCBITaxon:family +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9605 +name: Homo +namespace: ncbi_taxonomy +synonym: "humans" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:207598 ! Homininae +property_value: has_rank NCBITaxon:genus +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9606 +name: Homo sapiens +namespace: ncbi_taxonomy +synonym: "Home sapiens" RELATED misspelling [] +synonym: "Homo sampiens" RELATED misspelling [] +synonym: "Homo sapeins" RELATED misspelling [] +synonym: "Homo sapian" RELATED misspelling [] +synonym: "Homo sapians" RELATED misspelling [] +synonym: "Homo sapien" RELATED misspelling [] +synonym: "Homo sapience" RELATED misspelling [] +synonym: "Homo sapiense" RELATED misspelling [] +synonym: "Homo sapients" RELATED misspelling [] +synonym: "Homo sapines" RELATED misspelling [] +synonym: "Homo spaiens" RELATED misspelling [] +synonym: "Homo spiens" RELATED misspelling [] +synonym: "human" EXACT genbank_common_name [] +synonym: "Humo sapiens" RELATED misspelling [] +synonym: "man" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9605 ! Homo +property_value: has_rank NCBITaxon:species +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: PATO:0000001 +name: quality +namespace: quality +alt_id: PATO:0000072 +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +synonym: "trait" EXACT [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000161 +name: rate +namespace: quality +def: "A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time." [PATOC:melissa] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002062 ! physical quality of a process +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001236 +name: process quality +namespace: quality +alt_id: PATO:0001239 +alt_id: PATO:0001240 +def: "A quality which inheres in an process." [PATOC:GVG] +comment: See comments of relational quality of a physical entity. +synonym: "quality of a process" EXACT [] +synonym: "quality of occurrent" EXACT [] +synonym: "quality of process" EXACT [] +synonym: "relational quality of occurrent" EXACT [] +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001241 +name: physical object quality +namespace: quality +alt_id: PATO:0001237 +alt_id: PATO:0001238 +def: "A quality which inheres in a continuant." [PATOC:GVG] +comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. +synonym: "monadic quality of a continuant" EXACT [] +synonym: "monadic quality of an object" NARROW [] +synonym: "monadic quality of continuant" NARROW [] +synonym: "multiply inhering quality of a physical entity" EXACT [] +synonym: "quality of a continuant" EXACT [] +synonym: "quality of a single physical entity" EXACT [] +synonym: "quality of an object" EXACT [] +synonym: "quality of continuant" EXACT [] +xref: snap:Quality +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001338 +name: mixed sex +namespace: quality +def: "A biological sex quality inhering in a population of multiple sexes." [MGED:MGED] +comment: For example a mixture of females and male or males and hermaphrodites. +subset: value_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001415 +name: morbidity +namespace: quality +def: "A quality inhering in a population by virtue of the proportion of its members that are ill at a given time." [PATOC:GVG] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002003 +name: population quality +namespace: quality +def: "A quality that inheres in an entire population or part of a population." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002062 +name: physical quality of a process +namespace: quality +subset: attribute_slim +is_a: PATO:0001236 ! process quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +created_by: george +creation_date: 2009-06-05T09:16:46Z + +[Term] +id: PCO:0000000 +name: collection of organisms +def: "A material entity that consists of two or more organisms, viruses, or viroids." [] +comment: May be of the same or different species. +is_a: BFO:0000027 ! object aggregate +is_a: PCO:0000031 ! organismal entity +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "group of organism" xsd:string +property_value: IAO:0000118 "organism collection" xsd:string + +[Term] +id: PCO:0000001 +name: population of organisms +def: "A collection of organisms, all of the same species, that live in the same place." [] +comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000112 "" xsd:string +property_value: IAO:0000112 "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 ISBN:0878932739 xsd:string + +[Term] +id: PCO:0000002 +name: ecological community +def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] +comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +property_value: IAO:0000118 "multispecies community" xsd:string +property_value: IAO:0000119 ISBN:0865423504 xsd:string + +[Term] +id: PCO:0000003 +name: quality of a population +def: "A quality that inheres in a biological population." [] +comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. +is_a: PATO:0002003 ! population quality +intersection_of: PATO:0002003 ! population quality +intersection_of: RO:0000052 PCO:0000001 ! population of organisms +relationship: RO:0000052 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000004 +name: quality of an ecological community +def: "A quality that inheres in a community." [] +comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. +is_a: PATO:0002003 ! population quality +intersection_of: PATO:0002003 ! population quality +intersection_of: RO:0000052 PCO:0000002 ! ecological community +relationship: RO:0000052 PCO:0000002 ! ecological community +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000005 +name: population process +def: "A process that has as primary participant a population. " [] +comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +is_a: BFO:0000015 ! process +relationship: RO:0000057 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000006 +name: population birth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000007 +name: population death rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000008 +name: population growth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string + +[Term] +id: PCO:0000009 +name: obsolete carrying capacity +def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] +is_a: ObsoleteClass +property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +property_value: IAO:0000119 ISBN:0878932739 xsd:string +property_value: IAO:0000231 IAO:0000423 +is_obsolete: true + +[Term] +id: PCO:0000010 +name: community species richness +def: "The number of different species represented in an ecological community." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string + +[Term] +id: PCO:0000011 +name: population growth +def: "A process that leads to a change in the number of individuals (positive or negative) in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000012 +name: logistic population growth +def: "A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000013 +name: exponential population growth +def: "A population growth process that leads to an exponential increase in the number of individuals in a population." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000014 +name: predator role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000015 +name: prey role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000016 +name: symbiont role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000017 +name: species as a collection of organisms +def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string + +[Term] +id: PCO:0000018 +name: single-species collection of organisms +def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000118 "collection of organisms of the same species" xsd:string + +[Term] +id: PCO:0000019 +name: community species diversity +def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] +comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string + +[Term] +id: PCO:0000020 +name: family +def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] +comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string +property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string + +[Term] +id: PCO:0000021 +name: population extinction +def: "A population process that ultimately leads to the death of all individuals in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000022 +name: species extinction +def: "A process that ultimately leads to the death of all individuals in a population." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000023 +name: community species evenness +def: "A quality of a community that reflects how close in abundance all species in a community are." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_evenness" xsd:string + +[Term] +id: PCO:0000024 +name: household +def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] +is_a: PCO:0000031 ! organismal entity +relationship: RO:0002321 ENVO:01000744 ! human dwelling +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! Homo sapiens +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string + +[Term] +id: PCO:0000025 +name: red population +comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000026 +name: red organism +comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000027 +name: collection of humans +def: "A collection of organisms of the same species that has as members only humans." [] +is_a: PCO:0000018 ! single-species collection of organisms +intersection_of: PCO:0000018 ! single-species collection of organisms +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! Homo sapiens +relationship: RO:0002351 NCBITaxon:9606 ! Homo sapiens +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "human community" xsd:string +property_value: IAO:0000118 "human population" xsd:string + +[Term] +id: PCO:0000028 +name: community +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). +is_a: ObsoleteClass +property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000029 +name: multi-species collection of organisms +def: "A collection of organisms that consists of two or more organisms from at least two species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string + +[Term] +id: PCO:0000030 +name: agricultural household +name: obsolete organismal entity +def: "A household in which the majority of the income of its members is derived from agricultural activities." [] +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: ObsoleteClass +is_a: PCO:0000024 ! household +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string +property_value: IAO:0000231 "wrong IRI form" xsd:string +is_obsolete: true +replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 + +[Term] +id: PCO:0000031 +name: organismal entity +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: BFO:0000040 ! material entity +union_of: CARO:0001010 ! organism or virus or viroid +union_of: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 + +[Term] +id: PCO:0000032 +name: biological family +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +is_a: PCO:0000020 ! family +property_value: IAO:0000118 "genealogical family" xsd:string +property_value: IAO:0000119 "Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/" xsd:string + +[Term] +id: PCO:0000033 +name: human social gathering activity +def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] +is_a: GO:0035176 ! social behavior +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000034 +name: human community event +def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000035 +name: party +def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000037 +name: potluck +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string +property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000038 +name: wedding +def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000039 +name: baby shower +def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000040 +name: tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: PCO:0000002 ! ecological community +relationship: BFO:0000050 ENVO:01001369 ! tidal mangrove shrubland +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string + +[Term] +id: PCO:0000041 +name: invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: PATO:0001241 ! physical object quality + +[Term] +id: PCO:0000042 +name: microbe +synonym: "microbial organism" EXACT [] +is_a: CARO:0001010 ! organism or virus or viroid +relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye + +[Term] +id: PCO:0000043 +name: collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe +intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000044 +name: multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: PCO:0000029 ! multi-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000045 +name: single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000046 +name: microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: PCO:0000001 ! population of organisms +is_a: PCO:0000045 ! single species collection of microbes +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0001000 +name: pair of interacting organisms +def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] +is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid + +[Term] +id: PCO:0001001 +name: pair of interacting organisms of the same species +is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0001000 ! pair of interacting organisms + +[Term] +id: PCO:1000000 +name: migratory population +def: "A population which is participating in a migration process." [] +is_a: PCO:0000001 ! population of organisms +relationship: RO:0000056 PCO:1000001 ! population migration +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:1000001 +name: population migration +def: "A population process during which a population moves from one area to another." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Migration xsd:string + +[Term] +id: PCO:1000002 +name: human population migration +def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration +is_a: PCO:1000001 ! population migration +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000003 +name: human migratory population +def: "A migratory population of humans, travelling with the intention of settling in a new area." [] +is_a: PCO:0000027 ! collection of humans +relationship: RO:0000056 PCO:1000002 ! human population migration +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000004 +name: microbial community +def: "An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness." [] +comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. +synonym: "microbiota" BROAD [] +is_a: PCO:0000002 ! ecological community +is_a: PCO:0000044 ! multi-species collection of microbes +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string +property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Synonym +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: SynonymType +is_a: IAO:0000102 ! data about an ontology part + diff --git a/pco.owl b/pco.owl index 26ca49d..205fa6e 100644 --- a/pco.owl +++ b/pco.owl @@ -1,37 +1,27 @@ - - - - - - - - - - - The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. + xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> + + http://orcid.org/0000-0002-4366-3088 - Ramona Walls + https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg + Ramona Walls http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. @@ -53,6 +43,22 @@ + + + + + + + + + + + + + + + + @@ -71,9 +77,10 @@ example - A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage @@ -132,6 +139,7 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition @@ -146,6 +154,8 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + editor note editor note @@ -157,7 +167,7 @@ We also have the outstanding issue of how to aim different definitions to differ term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor @@ -187,6 +197,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source @@ -216,6 +227,34 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + @@ -276,10 +315,8 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. first order logic expression - An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. PERSON:Alan Ruttenberg first order logic expression - @@ -382,6 +419,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + elucidation @@ -394,6 +432,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language + has associated axiom(nl) @@ -406,6 +445,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax + has associated axiom(fol) @@ -423,6 +463,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + 2018-09-21T16:43:39Z + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + @@ -430,6 +498,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + has axiom label @@ -461,11061 +530,1169 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + - - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation - https://github.com/oborel/obo-relations/wiki/ROAndTime - + + - + - - tooth SubClassOf 'never in taxon' value 'Aves' - x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - Chris Mungall - - - ?X DisjointWith RO_0002162 some ?Y - never in taxon - - - + - + - - A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. - non-overlapping with - shares no parts with - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) - mutually spatially disjoint with - - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - + - + - - An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. - taxonomic class assertion - - - + - + - - S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] - ambiguous for taxon - - - + - + - - S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - https://orcid.org/0000-0002-6601-2165 - - This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost - dubious for taxon - - - + - + - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - https://orcid.org/0000-0002-6601-2165 - - present in taxon - - - + - + - - defined by inverse - - + - + - - An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. - logical macro assertion - https://github.com/oborel/obo-relations/wiki/ShortcutRelations - + - + - - An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. - annotation property cardinality - - - + - + - - A logical macro assertion whose domain is an IRI for a class - The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL - logical macro assertion on a class - - + - + - - A logical macro assertion whose domain is an IRI for a property - logical macro assertion on a property - - + - + - - logical macro assertion on an object property - - + - + - - logical macro assertion on an annotation property - - + - + - - An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. - dispositional interpretation - - + - + - - 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' - A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. - shares no connection with - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) - has no connections with - - + - + - - inherited annotation property - + - + - - Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) - curator guidance link - - + - + - - brain always_present_in_taxon 'Vertebrata' - forelimb always_present_in_taxon Euarchontoglires - S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S - This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. - never lost in - always present in taxon - + + - + - - This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. - temporal logical macro assertion on a class - + + - + - - measurement property has unit - + + + has_alternative_id - + - - has start time value - - + - + - - has end time value - + + - + - - Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. - start, days post fertilization - + + + has_exact_synonym - + - - Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. - end, days post fertilization - + + - + - - Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. - start, years post birth - + + + has_obo_namespace - + - - Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 - end, years post birth - + + + has_related_synonym - + - - Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. - start, months post birth - + + - + - - Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 - end, months post birth - + + - + - - Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. - month of gestation - + + + in_subset - + - - A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process - has developmental stage marker - + + - + - - Count of number of days intervening between the start of the stage and the time of coitum. - For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) - start, days post coitum - - + + + - + - - Count of number of days intervening between the end of the stage and the time of coitum. - end, days post coitum - + + - + - - start, weeks post birth - - + + + - + - - end, weeks post birth - - - + - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p - is asymmetric relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - + + + - + - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p - is symmetric relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - + + + - + - - R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process - is relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - + - - relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y - The general property hierarchy is: + + - "directly P" SubPropertyOf "P" - Transitive(P) -Where we have an annotation assertion + - "directly P" "is direct form of" "P" - If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - Chris Mungall - is direct form of - - + - + - - relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y - Chris Mungall - is indirect form of - - + - + - - logical macro assertion on an axiom - - + - + - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - + - + - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - + - + - - An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. - is relational form of a class - - + - + - - A shortcut relationship that holds between two entities based on their identity criteria - logical macro assertion involving identity - - + - + - - A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. - in approximate one to one relationship with - - + - + - - x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y - The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" - is approximately equivalent to - - + - + - - 'anterior end of organism' is-opposite-of 'posterior end of organism' - 'increase in temperature' is-opposite-of 'decrease in temperature' - x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - is opposite of - - - + - - x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - is indistinguishable from - - + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + - + - - evidential logical macro assertion on an axiom - - + + + + continuant + Continuant + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + - + - - A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. - axiom has evidence - - + + + occurrent + Occurrent + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + - + - - A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. - axiom contradicted by evidence - - + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + - - - - In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. - this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. - If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion - is representative IRI for equivalence set - OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member - - - - - - - - - eco subset - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - subset_property - - - - - - - - - - - - - - - - - - - - has_broad_synonym - - - - - - - - database_cross_reference - - - - - - - - has_exact_synonym - - - - - - - - - - - - - - has_obo_format_version - - - - - - - - has_related_synonym - - - - - - - - - - - - - - - - - - - - in_subset - - - - - - - - shorthand - - - - - - - - - - - - - - is defined by - - - - - is defined by - This is an experimental annotation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - - - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - accidentally included in BFO 1.2 proposal - - should have been BFO_0000062 - obsolete preceded by - - - - - - - - - - - - - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - precedes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - sardine has consumer some homo sapiens - - 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. - Damion Dooley - has consumer - - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - bearer of - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - inverse of has disposition - - disposition of - - - - - - - - - - A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. - David Osumi-Sutherland - (forall (?x ?y) - (iff - (neural_circuit_path ?x ?y) - (and - ("neuron ; CL_0000540" ?x) - ("neuron ; CL_0000540" ?y) - (or - (synapsed_by ?x ?y) - (synapsed_to ?x ?y))))) - -(forall (...s ?x ?y ?z) - (iff - (neural_circuit_path ...s ?x ?y ?z) - (and - (neural_circuit_path ...s ?x ?y) - ("neuron ; CL_0000540" ?z) - (or - (synapsed_by ?y ?z) - (synapsed_to ?y ?z))))) - -(forall (?x ?y) - (iff - (in_neural_circuit_with ?x ?y) - (exists (...s) - (neural_circuit_path ?x ...s ?y)))) - - - in neural circuit with - - - - - - - - - - - A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. - David Osumi-Sutherland - (forall (?x ?y) - (iff - (upstream_neural_circuit_path ?x ?y) - (and - ("neuron ; CL_0000540" ?x) - ("neuron ; CL_0000540" ?y) - (synapsed_to ?x ?y)))) - - -(forall (...s ?x ?y ?z) - (iff - (upstream_neural_circuit_path ...s ?x ?y ?z ) - (and - (upstream_neural_circuit_path ...s ?x ?y) - ("neuron ; CL_0000540" ?z) - (synapsed_to ?y ?z)))) - -(forall (?x ?y) - (iff - (upstream_in_neural_circuit_with ?x ?y) - (exists (...s) - (upstream_neural_circuit_path ?x ...s ?y)))) - - - upstream in neural circuit with - - - - - - - - - - - A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. - David Osumi-Sutherland - (forall (?x ?y) - (iff - (downstream_neural_circuit_path ?x ?y) - (and - ("neuron ; CL_0000540" ?x) - ("neuron ; CL_0000540" ?y) - (synapsed_by ?x ?y)))) - - -(forall (...s ?x ?y ?z) - (iff - (downstream_neural_circuit_path ...s ?x ?y ?z ) - (and - (downstream_neural_circuit_path ...s ?x ?y) - ("neuron ; CL_0000540" ?z) - (synapsed_by ?y ?z)))) - -(forall (?x ?y) - (iff - (downstream_in_neural_circuit_with ?x ?y) - (exists (...s) - (downstream_neural_circuit_path ?x ...s ?y)))) - - - - downstream in neural circuit with - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. - - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - location_of - - location of - - - - - - - - - - - - - - - contained in - Containment is location not involving parthood, and arises only where some immaterial continuant is involved. - Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - - contained_in - - - contained in - - - - - - - - contains - - - contains - - - - - - - - - - - penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - is allergic trigger for - - - - - - - - - - - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - is autoimmune trigger for - - - - - - - - - - penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - has allergic trigger - - - - - - - - - - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - has autoimmune trigger - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - located in - - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - David Osumi-Sutherland - - aligned with - - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - David Osumi-Sutherland - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland - - electrically_synapsed_to - - - - - - - - - The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - David Osumi-Sutherland - tracheates - - - - - - - - - David Osumi-Sutherland - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - innervated_by - - - - - - - - - - David Osumi-Sutherland - has synaptic terminal of - - - - - - - - - - - - - - - - - - - - - X outer_layer_of Y iff: -. X :continuant that bearer_of some PATO:laminar -. X part_of Y -. exists Z :surface -. X has_boundary Z -. Z boundary_of Y - -has_boundary: http://purl.obolibrary.org/obo/RO_0002002 -boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - - A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. - bounding layer of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. - Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland - - Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. - coincident with - - - - - - - - - - A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. - David Osumi-Sutherland - x 'cell expresses' y iff: -cell(x) -AND gene(y) -AND exists some 'transcription, DNA templated (GO_0006351)'(t) -AND t occurs_in x -AND t has_input y - cell expresses - - - - - - - - - - - x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland - regulates in other organism - - - - - - - - - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - David Osumi-Sutherland - - regulates transport of - - - - - - - - - - - - A part of relation that applies only between occurents. - occurent part of - - - - - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - has positive regulatory component activity - - - - - - - - - - dos - 2017-05-24T09:36:08Z - A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. - has necessary component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - has component activity - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - has component process - - - - - - - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos - 2017-07-19T17:30:36Z - has ligand - - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - GOC:dos - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - David Osumi-Sutherland - <= - - Primitive instance level timing relation between events - before or simultaneous with - - - - - - - - - - David Osumi-Sutherland - - t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with - - - - - - - - - - David Osumi-Sutherland - - t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) - before - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which ends - - - - - - - - - - - David Osumi-Sutherland - di - Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - encompasses - - - - - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - ends after - - - - - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - immediately preceded by - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which starts - - - - - - - - - - - - - - David Osumi-Sutherland - - starts before - - - - - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - immediately precedes - - - - - - - - - - - David Osumi-Sutherland - io - - X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) - starts during - - - - - - - - - - David Osumi-Sutherland - d - during - - X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) - happens during - - - - - - - - - David Osumi-Sutherland - o - overlaps - - X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). - ends during - - - - - - - - - - - - - - - Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - - has soma location - - - - - - - - - - - - - - - - - - - - - - - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - David Osumi-Sutherland - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - fasciculates with - - - - - - - - - - - - - - - - Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( - <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - - axon synapses in - - - - - - - - - - - - - - - - - - - - - - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - synapsed by - - - - - - - - - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - - has plasma membrane part - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_Ib_bouton_to - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_Is_bouton_to - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_II_bouton_to - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_II_bouton - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_Ib_bouton - - - - - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland - synapsed in - http://purl.obolibrary.org/obo/BFO_0000051 some ( - http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( - http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - - has postsynaptic terminal in - - - - - - - - - - has neurotransmitter - releases neurotransmitter - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_Is_bouton - - - - - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - - has presynaptic terminal in - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type III bouton. - BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_III_bouton_to - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type III bouton. - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_III_bouton - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - Chris Mungall - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - N1 synapsed_to some N2 -Expands to: -N1 SubclassOf ( - has_part some ( - ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( - ‘synapse ; GO:0045202’ that has_part some ( - ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) - synapsed to - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - - - Chris Mungall - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( - http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( - <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - - dendrite synapsed in - - - - - - - - - - - - - - - - - - - - - - - - - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland - has synapse in - <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - - has synaptic terminal in - - - - - - - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - - - overlaps - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - - has fasciculating neuron projection - - - - - - - - - - - - - - - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. -T innervates some R -Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - innervates - - - - - - - - - - - - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - continuous with - FMA:85972 - - - - - - - - - - x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x - We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) - (iff - (proper_overlaps ?x ?y) - (and - (overlaps ?x ?y) - (not (part_of ?x ?y)) - (not (part_of ?y ?x))))) - - - partially overlaps - - - - - - - - - - - - d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. - ancestral_stucture_of - evolutionarily_descended_from - derived by descent from - - - - - - - - - - - inverse of derived by descent from - - has derived by descendant - - - - - - - - - - - - - - - - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - VBO calls this homologous_to - shares ancestor with - - - - - - - - - - - - serially homologous to - - - - - - - - - lactation SubClassOf 'only in taxon' some 'Mammalia' - - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. - The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. - - 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - Chris Mungall - - - only in taxon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - Chris Mungall - Jennifer Deegan - - - - Connects a biological entity to its taxon of origin. - in taxon - - - - - - - - - - - A is spatially_disjoint_from B if and only if they have no parts in common - There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy - BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - - - spatially disjoint from - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - - - - - - - - - - - - - - - - - - - - - - - - - - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - connected to - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - - - - - - - - - - - - - - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - connects - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - - - - - - - - - - - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of - - - - - - - - - true - - - - - - - - - Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - supplies - - - - - - - - - Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - drains - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - has component - - - - - - - - - - - - - A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall - - has phenotype - - - - - - - - - - - inverse of has phenotype - Chris Mungall - - - phenotype of - - - - - - - - - - - - - - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan - This is the transitive form of the develops from relation - develops from - - - - - - - - - - - - - inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan - - develops into - - - - - - - - - - - - - - - - - definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" - We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. - Chris Mungall - gene product of - - - - - - - - - - - - - - - every HOTAIR lncRNA is the gene product of some HOXC gene - every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene - - x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y - Chris Mungall - has gene product - - - - - - - - - - - - - - - - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - Chris Mungall - expressed in - - - - - - - - - - - - - - - - - - - - - - - - - - - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y - Chris Mungall - David Osumi-Sutherland - has developmental precursor - FBbt - - TODO - add child relations from DOS - directly develops from - - - - - - - - - - A parasite that kills or sterilizes its host - parasitoid of - - - - - - - - - inverse of parasitoid of - - has parasitoid - - - - - - - - - - inverse of directly develops from - developmental precursor of - - directly develops into - - - - - - - - - - - - - - - - - - - - - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit - Chris Mungall - David Hill - Tanya Berardini - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - regulates - - - - - - - - - - - - - - - - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. - Chris Mungall - - negatively regulates (process to process) - negatively regulates - - - - - - - - - - - - - - - - - - - - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. - Chris Mungall - - positively regulates (process to process) - positively regulates - - - - - - - - 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) - heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') - - x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. - Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) - This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - Chris Mungall - has prototype - - - - - - - - - - - - - - - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' - - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) - - capable of - - - - - - - - - - - - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall - has function in - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) - capable of part of - - - - - - - - - true - - - - - - - - - - - x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall - agent in - actively participates in - - - - - - - - - 'heart development' has active participant some Shh protein - - x has participant y if and only if x realizes some active role that inheres in y - This may be obsoleted and replaced by the original 'has agent' relation - Chris Mungall - has agent - - has active participant - - - - - - - - - - - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall - - surrounded by - - - - - - - - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - - x adjacent to y if and only if x and y share a boundary. - This relation acts as a join point with BSPO - Chris Mungall - - adjacent to - - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - - - - - - - - - - inverse of surrounded by - Chris Mungall - - - surrounds - - - - - - - - - - - Chris Mungall - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporally related to - - - - - - - - - - - - inverse of starts with - Chris Mungall - Allen - - starts - - - - - - - - - - - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall - started by - - starts with - - - - - - - - - - - - - - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall - develops from part of - - - - - - - - - - - - - - - x develops_in y if x is located in y whilst x is developing - Chris Mungall - EHDAA2 - Jonathan Bard, EHDAA2 - develops in - - - - - - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - obligate parasite of - - - - - - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - facultative parasite of - - - - - - - - - - - - inverse of ends with - Chris Mungall - - ends - - - - - - - - - - - - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall - finished by - - ends with - - - - - - - - - - - - - - - - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall - starts with process that occurs in - - has start location - - - - - - - - - - - - - - - - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall - ends with process that occurs in - - has end location - - - - - - - - - - - - - - - - - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall - consumes - - has input - - - - - - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. - Chris Mungall - produces - - has output - - - - - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - stem parasite of - - - - - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - root parasite of - - - - - - - - - A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. - hemiparasite of - - - - - - - - - A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. - ExO:0000001 - has exposure receptor - - - - - - - - - A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. - ExO:0000000 - has exposure stressor - - - - - - - - - A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor - ExO:0000055 - has exposure route - - - - - - - - - A broad relationship between an exposure event or process and the course takes from the source to the target. - http://purl.obolibrary.org/obo/ExO_0000004 - has exposure transport path - - - - - - - - - - Any relationship between an exposure event or process and any other entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. - related via exposure to - - - - - - - - - g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. - over-expressed in - - - - - - - - - g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. - under-expressed in - - - - - - - - - - Any portion of roundup 'has active ingredient' some glyphosate - A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. - has active substance - has active pharmaceutical ingredient - has active ingredient - - - - - - - - - inverse of has active ingredient - - active ingredient in' - - - - - - - - - - b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - connecting branch of - - - - - - - - - inverse of connecting branch of - - has connecting branch - - - - - - - - - - - - - - - - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - - x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall - has developmental contribution from - - - - - - - - - - - - - - - inverse of has developmental contribution from - Chris Mungall - - developmentally contributes to - - - - - - - - - - - - - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - developmentally induced by - - - - - - - - - - - Inverse of developmentally induced by - Chris Mungall - developmentally induces - - - - - - - - - - - - - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p - false - Chris Mungall - In general you should not use this relation to make assertions - use one of the more specific relations below this one - This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by - - - - - - - - - c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) - has biological role - - - - - - - - - c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) - has application role - - - - - - - - - c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) - has chemical role - - - - - - - - - - - - - c involved in regulation of p if c enables 'p' and p' causally upstream of p - acts upstream of - - - - - - - - - - - - - c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p - affects - acts upstream of or within - - - - - - - - - - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else - This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall - replaces - developmentally replaces - - - - - - - - - - Inverse of developmentally preceded by - Chris Mungall - developmentally succeeded by - - - - - - - - - - - - - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - Chris Mungall - part of developmental precursor of - - - - - - - - - - - x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x - Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. - Chris Mungall - ubiquitously expressed in - - - - - - - - - - Inverse of 'expressed in' - Chris Mungall - expresses - - - - - - - - - - inverse of ubiquiotously expressed in - Chris Mungall - - ubiquitously expresses - - - - - - - - - - - - p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). - This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall - results_in_developmental_progression_of - results in developmental progression of - - - - - - - - - - - every flower development (GO:0009908) results in development of some flower (PO:0009046) - - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml - results_in_development_of - results in development of - - - - - - - - - - - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_formation_of - results in formation of - - - - - - - - - - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_morphogenesis_of - results in morphogenesis of - - - - - - - - - - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_maturation_of - results in maturation of - - - - - - - - - foramen ovale closure SubClassOf results in disappearance of foramen ovale - - Chris Mungall - May be merged into parent relation - results_in_disappearance_of - results in disappearance of - - - - - - - - - every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - - Chris Mungall - May be merged into parent relation - results in developmental regression of - - - - - - - - - - Inverse of 'is substance that treats' - cjm - - is treated by substance - - - - - - - - - - - Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' -where -'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview - - x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg - adapted for living in - - A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. - has habitat - - - - - - - - - cjm - holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y - causally upstream of, positive effect - - - - - - - - - cjm - holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y - causally upstream of, negative effect - - - - - - - - - A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm - 2017-06-05T17:35:04Z - has exposure stimulus - - - - - - - - - Chris Mungall - evolutionary variant of - - - - - - - - - - - - - - Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c - Chris Mungall - regulates location of - transports - transports or maintains localization of - - - - - - - - - - - - - - - - - q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. - Because part_of is transitive, inheres in is a sub-relation of inheres in part of - Chris Mungall - - - inheres in part of - - - - - - - - - true - - - - - - - - - - - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. - The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_acquisition_of_features_of - results in acquisition of features of - - - - - - - - A relationship that holds via some environmental process - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. - evolutionarily related to - - - - - - - - A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions - - ecologically related to - - - - - - - - - An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall - adapted for - - confers advantage in - - - - - - - - A mereological relationship or a topological relationship - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - - mereotopologically related to - - - - - - - - A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development - developmentally related to - - - - - - - - - - - Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) - a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall - http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with - In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium - colocalizes with - - - - - - - - - - ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. - Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. - eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex - We would like to say - -if and only if - exists c', p' - c part_of c' and c' capable_of p - and - c capable_of p' and p' part_of p -then - c contributes_to p - -However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall - http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to - In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. - contributes to - - - - - - - - - - - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity - Chris Mungall - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. - enables - - - - - - - - Chris Mungall - This is a grouping relation that collects relations used for the purpose of connecting structure and function - functionally related to - - - - - - - - - - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall - false - part of structure that is capable of - - - - - - - - - true - - - - - - - - - - holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism - genomically related to - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall - actively involved in - enables part of - involved in - - - - - - - - - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid - p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall - - regulates levels of (process to entity) - regulates levels of - - - - - - - - - - - - - - inverse of enables - Chris Mungall - enabled by - - - - - - - - - - - - inverse of regulates - Chris Mungall - regulated by (processual) - - regulated by - - - - - - - - - inverse of negatively regulates - Chris Mungall - - negatively regulated by - - - - - - - - - inverse of positively regulates - Chris Mungall - - positively regulated by - - - - - - - - - - A relationship that holds via some process of localization - Chris Mungall - related via localization to - - - - - - - - - - - - - This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall - has target start location - - - - - - - - - - - - - This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall - has target end location - - - - - - - - - - - - - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall - imports - - - - - - - - - Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall - results in transport along - - - - - - - - - Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall - results in transport across - - - - - - - - - - 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall - results in growth of - - - - - - - - - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall - results in transport to from or in - - - - - - - - - - - - - Chris Mungall - exports - - - - - - - - - - an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. - p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in commitment to - - - - - - - - - - p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in determination of - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - inverse of has input - Chris Mungall - - - input of - - - - - - - - - - inverse of has output - Chris Mungall - - - output of - - - - - - - - - Chris Mungall - formed as result of - - - - - - - - - - A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall - results in structural organization of - - - - - - - - - - The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in specification of - - - - - - - - - p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall - results in developmental induction of - - - - - - - - - Chris Mungall - http://neurolex.org/wiki/Property:DendriteLocation - has dendrite location - - - - - - - - - - - a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall - - attached to - - - - - - - - - - m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall - Wikipedia:Insertion_(anatomy) - has muscle origin - - - - - - - - - - - m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall - Wikipedia:Insertion_(anatomy) - has muscle insertion - - - - - - - - - - false - - x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat - Chris Mungall - Chris Mungall - - A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. - has fused element - - - - - - - - - - - - - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with - - https://github.com/obophenotype/uberon/issues/170 - - - - - - - - - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - - tributary of - - http://en.wikipedia.org/wiki/Tributary - - - - - - - - - Deschutes River distributary_of Little Lava Lake - - x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall - branch of - distributary channel of - http://en.wikipedia.org/wiki/Distributary - - This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes - distributary of - - - - - - - - - - - - - - - - - x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall - anastomoses with - - anabranch of - - - - - - - - - - - - - - - A lump of clay and a statue - x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios - spatially coextensive with - - - - - - - - - - - - - - - - - - - - - - x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall - - branching part of - FMA:85994 - - - - - - - - - - x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall - - main stem of - - - - - - - - - - x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall - - proper distributary of - - - - - - - - - - x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall - - proper tributary of - - - - - - - - - - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall - has developmental potential involving - - - - - - - - - - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall - has potential to developmentally contribute to - - - - - - - - - - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall - has potential to developmentally induce - - - - - - - - - - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall - has potential to develop into - - - - - - - - - - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall - has potential to directly develop into - - - - - - - - - - - - - 'protein catabolic process' SubClassOf has_direct_input some protein - - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall - directly consumes - This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' - has direct input - - - - - - - - - Chris Mungall - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect input - true - - - - - - - - translation SubClassOf has_direct_output some protein - - p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. - Chris Mungall - directly produces - obsolete has direct output - true - - - - - - - - - - - - - - Chris Mungall - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - - - - - - - - - inverse of upstream of - Chris Mungall - causally downstream of - - - - - - - - - - - - Chris Mungall - immediately causally downstream of - - - - - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - directly activates - - - - - - - - - - - - - - - - - - - - - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - indirectly positively regulates - - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - directly inhibits - - - - - - - - - - - - - - - - - - - - - - - Chris Mungall - indirectly negatively regulates - - indirectly inhibits - - - - - - - - - - This relation groups causal relations between material entities and causal relations between processes - This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. - -To define causal relations in an activity-flow type network, we make use of 3 primitives: - - * Temporal: how do the intervals of the two occurrents relate? - * Is the causal relation regulatory? - * Is the influence positive or negative - -The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. - -For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. - -For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. - -Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causally related to - - - - - - - - - - - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain - Chris Mungall - causally upstream of - - - - - - - - - - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. - Chris Mungall - - immediately causally upstream of - - - - - - - - - - - - - - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall - - directly provides input for (process to process) - directly provides input for - - - - - - - - - - - - - transitive form of directly_provides_input_for - Chris Mungall - This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') - transitively provides input for (process to process) - transitively provides input for - - - - - - - - - - - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. - We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall - influences (processual) - affects - causally upstream of or within - - - - - - - - false - Chris Mungall - This is an exploratory relation - differs in - https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions - - - - - - - - - - - - - - - - - Chris Mungall - differs in attribute of - - - - - - - - - - Chris Mungall - differs in attribute - - - - - - - - - - inverse of causally upstream of or within - Chris Mungall - - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some 'p' and p' regulates some p - Chris Mungall - involved in regulation of - - - - - - - - - - - - - - - - - Chris Mungall - involved in positive regulation of - - - - - - - - - - - - - - - - - Chris Mungall - involved in negative regulation of - - - - - - - - - - - c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p - Chris Mungall - involved in or reguates - involved in or involved in regulation of - - - - - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d - Chris Mungall - executes activity in - enables activity in - - - - - - - - - true - - - - - - - - - p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall - contributes to morphology of - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - Considering relabeling as 'pairwise interacts with' - This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. - in pairwise interaction with - - interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - - An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall - genetically interacts with - - http://purl.obolibrary.org/obo/MI_0208 - - - - - - - - - - An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. - Chris Mungall - binds - molecularly binds with - molecularly interacts with - - http://purl.obolibrary.org/obo/MI_0915 - - - - - - - - - - - - - An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall - interacts with on organism level - - biotically interacts with - - http://eol.org/schema/terms/interactsWith - - - - - - - - - An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall - - trophically interacts with - - - - - - - - - - - A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] - Baleen whale preys on krill - An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz - is subject of predation interaction with - preys upon - - preys on - http://eol.org/schema/terms/preysUpon - http://www.inaturalist.org/observations/2942824 - - - - - - - - - - - - - - - - - A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - - - symbiotically interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - - commensually interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - - mutualistically interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - This relation groups a pair of inverse relations, parasite of and parasitized by - - - interacts with via parasite-host interaction - - - - - - - - - - - - - - - - - - Pediculus humanus capitis parasite of human - Chris Mungall - parasitizes - - direct parasite of - - parasite of - http://eol.org/schema/terms/parasitizes - - - - - - - - - - Chris Mungall - has parasite - parasitised by - directly parasitized by - - parasitized by - http://eol.org/schema/terms/hasParasite - - - - - - - - - Porifiera attaches to substrate - A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall - semibiotically interacts with - - participates in a abiotic-biotic interaction with - - - - - - - - - - - - - - - Axiomatization to GO to be added later - Chris Mungall - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. - phosphorylates - - - - - - - - - - - - - - - Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b - Chris Mungall - molecularly controls - - - - - - - - - - - - - - - - - - - Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. - Chris Mungall - inhibits - molecularly decreases activity of - - - - - - - - - - - - - - - - - - - Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. - Chris Mungall - activates - molecularly increases activity of - - - - - - - - - all dengue disease transmitted by some mosquito - A relationship that holds between a disease and organism - Add domain and range constraints - Chris Mungall - transmitted by - - - - - - - - - A relation that holds between a disease or an organism and a phenotype - Chris Mungall - has symptom - - - - - - - - - Chris Mungall - The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) - - host of - - - - - - - - - Chris Mungall - - has host - http://eol.org/schema/terms/hasHost - - - - - - - - - - Bees pollinate Flowers - This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall - is subject of pollination interaction with - - pollinates - http://eol.org/schema/terms/pollinates - - - - - - - - - Chris Mungall - has polinator - is target of pollination interaction with - - pollinated by - http://eol.org/schema/terms/hasPollinator - - - - - - - - - - Chris Mungall - Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. - - acquires nutrients from - - - - - - - - - inverse of preys on - Chris Mungall - has predator - is target of predation interaction with - - - preyed upon by - http://eol.org/schema/terms/HasPredator - http://polytraits.lifewatchgreece.eu/terms/PRED - - - - - - - - - - Anopheles is a vector for Plasmodium - Chris Mungall - a is a vector for b if a carries and transmits an infectious pathogen b into another living organism - - is vector for - - - - - - - - - Chris Mungall - - has vector - - - - - - - - - Chris Mungall - Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target - partner in - - - - - - - - - Chris Mungall - Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. - subject participant in - - - - - - - - - Chris Mungall - Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. - target participant in - - - - - - - - - Chris Mungall - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property - - - - - - - - - Chris Mungall - is symbiosis - - - - - - - - - Chris Mungall - is commensalism - - - - - - - - - Chris Mungall - is mutualism - - - - - - - - - Chris Mungall - is parasitism - - - - - - - - - Chris Mungall - - provides nutrients for - - - - - - - - - Chris Mungall - is subject of eating interaction with - - eats - - - - - - - - - Chris Mungall - eaten by - is target of eating interaction with - - is eaten by - - - - - - - - - - A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and -the a supports either the existence of b, or the truth value of b. - Chris Mungall - - is evidence for - - - - - - - - - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' - x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall - - - - composed primarily of - - - - - - - - - - - ABal nucleus child nucleus of ABa nucleus (in C elegans) - c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall - This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. - child nucleus of - - - - - - - - - A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall - child nucleus of in hermaphrodite - - - - - - - - - A child nucleus relationship in which the cells are part of a male organism - Chris Mungall - child nucleus of in male - - - - - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall - - has part that occurs in - - - - - - - - - true - - - - - - - - - - - - - - An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y - Axiomatization to GO to be added later - Chris Mungall - ubiquitinates - - - - - - - - - Chris Mungall - is kinase activity - - - - - - - - - Chris Mungall - is ubiquitination - - - - - - - - - - See notes for inverse relation - Chris Mungall - receives input from - - - - - - - - - This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall - sends output to - - - - - - - - - - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. - relation between structure and stage - - - - - - - - - - - - - - - - - - x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - Chris Mungall - existence starts during - - - - - - - - - x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - Chris Mungall - existence starts with - - - - - - - - - x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence overlaps - - - - - - - - - - x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts and ends during - - - - - - - - - - - - - - - - - - x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during - - - - - - - - - x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends with - - - - - - - - - - x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall - transformation of - - - - - - - - - - x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall - - immediate transformation of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts during or after - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during or before - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - - causal agent in - - - - - - - - - - - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between processes - - - - - - - - Chris Mungall - depends on - - - - - - - - - - q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 - This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. - Chris Mungall - - towards - - - - - - - - - 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate - p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall - has intermediate product - - has intermediate - - - - - - - - - - - The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between material entities - - - - - - - - - - - - - - A coral reef environment is determined by a particular coral reef - s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. - The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall - - determined by (system to material entity) - Chris Mungall - Pier Buttigieg - - determined by - - - - - - - - - inverse of determined by - Chris Mungall - determines (material entity to system) - - - determines - - - - - - - - - - - - - - - - s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall - - determined by part of - - - - - - - - - true - - - - - - - - - - x is transcribed from y if and only if x is synthesized from template y - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - transcribed from - - - - - - - - - inverse of transcribed from - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - transcribed to - - - - - - - - - x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - ribosomal translation of - - - - - - - - - inverse of ribosomal translation of - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - ribosomally translates to - - - - - - - - - - A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. - The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. - - sequentially related to - - - - - - - - - Every UTR is adjacent to a CDS of the same transcript - Two consecutive DNA residues are sequentially adjacent - Two exons on a processed transcript that were previously connected by an intron are adjacent - x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - sequentially adjacent to - - - - - - - - - - - Every CDS has as a start sequence the start codon for that transcript - x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall - started by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has start sequence - - - - - - - - - - inverse of has start sequence - Chris Mungall - starts - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - - is start sequence of - - - - - - - - - - - Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) - x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall - ended by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has end sequence - - - - - - - - - - inverse of has end sequence - Chris Mungall - ends - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - - is end sequence of - - - - - - - - - x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. - In the SO paper, this was defined as an instance-type relation - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - is consecutive sequence of - - - - - - - - - - Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. - x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall - - is sequentially aligned with - - - - - - - - - - - The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) - x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall - - bounds sequence of - - - - - - - - - - inverse of bounds sequence of - Chris Mungall - - - is bound by sequence of - - - - - - - - - - - - - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall - contains - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has subsequence - - - - - - - - - - - - inverse of has subsequence - Chris Mungall - contained by - - - is subsequence of - - - - - - - - - - - - - - - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall - - overlaps sequence of - - - - - - - - - - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall - disconnected from - - does not overlap sequence of - - - - - - - - - - inverse of downstream of sequence of - Chris Mungall - - is upstream of sequence of - - - - - - - - - - - x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall - - is downstream of sequence of - - - - - - - - - - A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript - x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall - - - is immediately downstream of sequence of - - - - - - - - - - A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript - inverse of immediately downstream of - Chris Mungall - - is immediately upstream of sequence of - - - - - - - - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' - A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - has skeleton - - - - - - - - - - p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall - results in ending of - - - - - - - - - - - - - - x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y - Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall - http://eol.org/schema/terms/hyperparasitoidOf - https://en.wikipedia.org/wiki/Hyperparasite - epiparasite of - hyperparasitoid of - - hyperparasite of - - - - - - - - - - - - - inverse of hyperparasite of - Chris Mungall - has epiparasite - has hyperparasite - hyperparasitoidized by - - - hyperparasitized by - - - - - - - - - Chris Mungall - http://en.wikipedia.org/wiki/Allelopathy - - allelopath of - http://eol.org/schema/terms/allelopathyYes - x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y - - - - - - - - - - Chris Mungall - - pathogen of - - - - - - - - - Chris Mungall - - has pathogen - - - - - - - - - inverse of is evidence for - Chris Mungall - - - - x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. - has evidence - - - - - - - - - - Chris Mungall - - causally influenced by (material entity to material entity) - causally influenced by - - - - - - - - - Chris Mungall - interaction relation helper property - - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - Chris Mungall - molecular interaction relation helper property - - - - - - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall - - results in movement of - - - - - - - - - - - - - - - - - - - Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b - Chris Mungall - - causally influences (material entity to material entity) - causally influences - - - - - - - - - A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. - biomechanically related to - - - - - - - - - m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall - Wikipedia:Antagonist_(muscle) - has muscle antagonist - - - - - - - - - inverse of branching part of - Chris Mungall - - - has branching part - - - - - - - - - - - x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - - conduit for - - - - - - - - - - x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall - GOC:cjm - - lumen of - - - - - - - - - - s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall - - luminal space of - - - - - - - - - A relation that holds between an attribute or a qualifier and another attribute. - Chris Mungall - - This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. - - has modifier - - - - - - - - - Chris Mungall - - participates in a biotic-biotic interaction with - - - - - - - - - - - - inverse of has skeleton - Chris Mungall - - skeleton of - - - - - - - - - - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - Chris Mungall - - directly regulates (processual) - - directly regulates - - - - - - - - - x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. - existence starts at point - - - - - - - - - - - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' - s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall - has part structure that is capable of - - - - - - - - - - p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. - results in closure of - - - - - - - - - p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p - results in breakdown of - - - - - - - - - results in synthesis of - - - - - - - - - - results in assembly of - - - - - - - - - p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. - results in catabolism of - - - - - - - - - - results in disassembly of - - - - - - - - - - results in remodeling of - - - - - - - - - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c - results in organization of - - - - - - - - - x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. - existence ends at point - - - - - - - - - - - A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall - - causal relation between material entity and a process - - - - - - - - - - - - - pyrethroid -> growth - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - - capable of negatively regulating - - - - - - - - - - - - - renin -> arteriolar smooth muscle contraction - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - - capable of positively regulating - - - - - - - - - pazopanib -> pathological angiogenesis - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. - treats - - The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. - capable of inhibiting or preventing pathological process - - - - - treats - Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship - - - - - - - - - benzene -> cancer [CHEBI] - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. - causes disease - - capable of upregulating or causing pathological process - - - - - - - - - c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. - treats - - is substance that treats - - - - - - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - is marker for - - - - - - - - - Inverse of 'causal agent in' - - has causal agent - - - - - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - related via dependence to - - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - correlated with - - - - - - - - - An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. - A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. - In the Gene Ontology association model, this corresponds to the With/From field - is evidence with support from - - - - - - - - - Inverse of is-model-of - has model - - - - - - - - related via evidence or inference to - - - - - - - - - - visits - https://github.com/oborel/obo-relations/issues/74 - - - - - - - - - visited by - - - - - - - - - - visits flowers of - - - - - - - - - has flowers visited by - - - - - - - - - - - lays eggs in - - - - - - - - - - has eggs laid in by - - - - - - - - - - https://github.com/jhpoelen/eol-globi-data/issues/143 - kills - - - - - - - - - is killed by - - - - - - - - - - Process(P1) directly regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. - - directly positively regulates (process to process) - directly positively regulates - - - - - - - - - - Process(P1) directly regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. - - directly negatively regulates (process to process) - directly negatively regulates - - - - - - - - - - A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host - - ectoparasite of - - - - - - - - - inverse of ectoparasite of - - has ectoparasite - - - - - - - - - - - A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system - lives inside of - endoparasite of - - - - - - - - - has endoparasite - - - - - - - - - - A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite - mesoparasite of - - - - - - - - - inverse of mesoparasite of - - has mesoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. - - intercellular endoparasite of - - - - - - - - - inverse of intercellular endoparasite of - - has intercellular endoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits host cells. - - intracellular endoparasite of - - - - - - - - - inverse of intracellular endoparasite of - - has intracellular endoparasite - - - - - - - - - - - - - - - - - - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - Melissa Haendel - - Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. - produces - - - - - - - - - - - a produced_by b iff some process that occurs_in b has_output a. - Melissa Haendel - - produced by - - - - - - - - - Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. - Logical axioms to be added after the relevant branch of GO is MIREOTed in - represses expression of - - - - - - - - - Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. - Logical axioms to be added after the relevant branch of GO is MIREOTed in - increases expression of - - - - - - - - Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? - Matthew Brush - The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. - is model of - - - - - - - - - The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. - -An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. - Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - causes or contributes to condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. - causes condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. - contributes to condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. - contributes to expressivity of condition - contributes to severity of condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. - contributes to penetrance of condition - contributes to frequency of condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. - is preventative for condition - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - ameliorates condition - - - - - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - correlated with condition - - - - - - - - - A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. - exacerbates condition - - - - - - - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. - condition ameliorated by - - - - - - - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. - condition exacerbated by - - - - - - - - - - An interaction relationship wherein a plant or algae is living on the outside surface of another plant. - https://en.wikipedia.org/wiki/Epiphyte - epiphyte of - - - - - - - - - inverse of epiphyte of - - has epiphyte - - - - - - - - - - A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material - https://en.wikipedia.org/wiki/Kleptoparasitism - kleptoparasite of - - - - - - - - - inverse of kleptoparasite of - - kleptoparasitized by - - - - - - - - - An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. - creates habitat for - - - - - - - - - - An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. - co-occurs - - - - - - - - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - lays eggs on - - - - - - - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - has eggs laid on by - - - - - - - - - muffin 'has substance added' some 'baking soda' - - "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - Damion Dooley - has substance added - - - - - - - - - 'egg white' 'has substance removed' some 'egg yolk' - - "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. - Damion Dooley - has substance removed - - - - - - - - - sardines 'immersed in' some 'oil and mustard' - - "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. - Damion Dooley - immersed in - - - - - - - - - - bread 'has primary substance added' some 'flour' - - 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. - Damion Dooley - has primary substance added - - - - - - - - - - - - - - - A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. - Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. - r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte - realized in response to - https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit - - - - - - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - - ECO:0000041 - SO:similar_to - sameness - similar to - correspondence - resemblance - in similarity relationship with - - - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - BGEE:curator - - - - - correspondence - - - - - - - - - - - - - Similarity that results from common evolutionary origin. - - - homologous to - This broad definition encompasses all the working definitions proposed so far in the literature. - in homology relationship with - - - - - - Similarity that results from common evolutionary origin. - - - - - - - - - - - - - - Similarity that results from independent evolution. - - - homoplasous to - analogy - in homoplasy relationship with - - - - - - Similarity that results from independent evolution. - - - - - - - - - - - - - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - - ECO:0000075 - homocracous to - Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. - in homocracy relationship with - - - - - - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - - - - - - - - - - - - - Homoplasy that involves different underlying mechanisms or structures. - - - analogy - Convergence usually implies a notion of adaptation. - in convergence relationship with - - - - - - Homoplasy that involves different underlying mechanisms or structures. - - - - - - - - - - - - Homoplasy that involves homologous underlying mechanisms or structures. - - - parallel evolution - Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. - in parallelism relationship with - - - - - - Homoplasy that involves homologous underlying mechanisms or structures. - - - - - - - - - - - - Homology that is defined by similarity with regard to selected structural parameters. - - - ECO:0000071 - MI:2163 - structural homologous to - idealistic homology - in structural homology relationship with - - - - - - Homology that is defined by similarity with regard to selected structural parameters. - - - - ISBN:0123195837 - - - - - - - - - - Homology that is defined by common descent. - - - homology - ECO:0000080 - RO_proposed_relation:homologous_to - SO:0000330 - SO:0000853 - SO:0000857 - SO:homologous_to - TAO:homologous_to - cladistic homology - historical homologous to - phylogenetic homology - taxic homology - true homology - in historical homology relationship with - - - - - - Homology that is defined by common descent. - - - ISBN:0123195837 - - - - - - - - - - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - - ECO:0000067 - biological homologous to - transformational homology - Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. - in biological homology relationship with - - - - - - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - - - - - - - - - - - - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - - atavism - rudiment - reversion - in reversal relationship with - - - - - - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - - - - - - - - - - - Structural homology that is detected by similarity in content and organization between chromosomes. - - - MeSH:Synteny - SO:0000860 - SO:0005858 - syntenic homologous to - synteny - in syntenic homology relationship with - - - - - - Structural homology that is detected by similarity in content and organization between chromosomes. - - MeSH:Synteny - - - - - - - - - - - Historical homology that involves genes that diverged after a duplication event. - - - SO:0000854 - SO:0000859 - SO:paralogous_to - paralogous to - in paralogy relationship with - - - - - - Historical homology that involves genes that diverged after a duplication event. - - - - - - - - - - - - - - - Paralogy that involves sets of syntenic blocks. - - - syntenic paralogous to - duplicon - paralogon - in syntenic paralogy relationship with - - - - - - Paralogy that involves sets of syntenic blocks. - - - DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y - - - - - - - - - - Syntenic homology that involves chromosomes of different species. - - - syntenic orthologous to - in syntenic orthology relationship with - - - - - - Syntenic homology that involves chromosomes of different species. - - - - - - - - - - - - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - - fractional homology - partial homologous to - segmental homology - mixed homology - modular homology - partial correspondence - percent homology - in partial homology relationship with - - - - - - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - ISBN:0123195837 - ISBN:978-0471984931 - - - - - - - - - - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - - MeSH:Structural_Homology,_Protein - protein structural homologous to - in protein structural homology relationship with - - - - - - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - - - - - - - - - - - - Structural homology that involves a pseudogenic feature and its functional ancestor. - - - pseudogene - SO:non_functional_homolog_of - non functional homologous to - in non functional homology relationship with - - - - - - Structural homology that involves a pseudogenic feature and its functional ancestor. - - SO:non_functional_homolog_of - - - - - - - - - - Historical homology that involves genes that diverged after a speciation event. - - - ECO:00000060 - SO:0000855 - SO:0000858 - SO:orthologous_to - orthologous to - The term is sometimes also used for anatomical structures. - in orthology relationship with - - - - - - Historical homology that involves genes that diverged after a speciation event. - - - - - - - - - - - - - - - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - - xenologous to - The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). - in xenology relationship with - - - - - - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - - - - - - - - - - - - Historical homology that involves two members sharing no other homologs in the lineages considered. - - - 1 to 1 homologous to - 1:1 homology - one-to-one homology - in 1 to 1 homology relationship with - - - - - - Historical homology that involves two members sharing no other homologs in the lineages considered. - - BGEE:curator - - - - - - - - - - - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - - 1 to 1 orthologous to - 1:1 orthology - one-to-one orthology - in 1 to 1 orthology relationship with - - - - - - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - - - - - - - - - - - - Paralogy that results from a whole genome duplication event. - - - ohnologous to - homoeology - in ohnology relationship with - - - - - - Paralogy that results from a whole genome duplication event. - - - - - - - - - - - - - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - - in-paralogous to - inparalogy - symparalogy - in in-paralogy relationship with - - - - - - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - - - - - - - - - - - Paralogy that results from a duplication preceding a given speciation event. - - - alloparalogy - out-paralogous to - outparalogy - in out-paralogy relationship with - - - - - - Paralogy that results from a duplication preceding a given speciation event. - - - - - - - - - - - - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - - pro-orthologous to - in pro-orthology relationship with - - - - - - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - - - - - - - - - - - - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - - semi-orthologous to - The converse of pro-orthologous. - in semi-orthology relationship with - - - - - - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - - - - - - - - - - - - Iterative homology that involves structures arranged along the main body axis. - - - serial homologous to - homonomy - in serial homology relationship with - - - - - - Iterative homology that involves structures arranged along the main body axis. - - - - - - - - - - - - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - - heterochronous homologous to - heterochrony - in heterochronous homology relationship with - - - - - - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - ISBN:978-0674639416 - - - - - - - - - - - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - - juvenification - pedomorphosis - in paedomorphorsis relationship with - - - - - - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - - ISBN:978-0674639416 - - - - - - - - - - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - in peramorphosis relationship with - - - - - - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - - - - - - - - - - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - in progenesis relationship with - - - - - - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - ISBN:978-0674639416 - - - - - - - - - - Paedomorphosis that is produced by a retardation of somatic development. - - - juvenilization - neotenous to - in neoteny relationship with - - - - - - Paedomorphosis that is produced by a retardation of somatic development. - - - ISBN:978-0674639416 - - - - - - - - - - Convergence that results from co-evolution usually involving an evolutionary arms race. - - - mimicrous to - in mimicry relationship with - - - - - - Convergence that results from co-evolution usually involving an evolutionary arms race. - - - - - - - - - - - - - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - - 1 to many orthologous to - 1:many orthology - one-to-many orthology - co-orthology - many to 1 orthology - in 1 to many orthology relationship with - - - - - - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - - - - - - - - - - - - Historical homology that involves two members of a larger set of homologs. - - - many to many homologous to - many-to-many homology - many:many homology - in many to many homology relationship with - - - - - - Historical homology that involves two members of a larger set of homologs. - - - - - - - - - - - - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - - 1 to many homologous to - one-to-many homology - 1:many homology - in 1 to many homology relationship with - - - - - - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - BGEE:curator - - - - - - - - - - - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - - apomorphous to - synapomorphy - in apomorphy relationship with - - - - - - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - ISBN:978-0252068140 - - - - - - - - - - Historical homology that is based on distant shared ancestry. - - - plesiomorphous to - symplesiomorphy - This term is usually contrasted to apomorphy. - in plesiomorphy relationship with - - - - - - Historical homology that is based on distant shared ancestry. - - ISBN:978-0252068140 - - - - - - - - - - - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - - deep genetic homology - deep homologous to - generative homology - homoiology - Used for structures in distantly related taxa. - in deep homology relationship with - - - - - - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - - - - - - - - - - - - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - - hemiplasous to - in hemiplasy relationship with - - - - - - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - - - - - - - - - - - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - - gametologous to - in gametology relationship with - - - - - - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - - - - - - - - - - - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - - MeSH:Chromosome_Pairing - chromosomal homologous to - in chromosomal homology relationship with - - - - - - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - ISBN:0195307615 - - - - - - - - - - - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - - many to many orthologous to - many-to-many orthology - many:many orthology - trans-orthology - co-orthology - trans-homology - in many to many orthology relationship with - - - - - - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - - - - - - - - - - - - - Paralogy that involves genes from the same species. - - - within-species paralogous to - in within-species paralogy relationship with - - - - - - Paralogy that involves genes from the same species. - - - - - - - - - - - - Paralogy that involves genes from different species. - - - between-species paralogous to - The genes have diverged before a speciation event. - in between-species paralogy relationship with - - - - - - Paralogy that involves genes from different species. - - - - - - - - - - - - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - - post-displacement - in postdisplacement relationship with - - - - - - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - - - - - - - - - - - Peramorphosis that is produced by a delay in the offset of development. - - - in hypermorphosis relationship with - - - - - - Peramorphosis that is produced by a delay in the offset of development. - - - ISBN:978-0674639416 - - - - - - - - - - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - - synologous to - in synology relationship with - - - - - - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - - - - - - - - - - - - - Orthology that involves functional equivalent genes with retention of the ancestral function. - - - ECO:0000080 - isoorthologous to - in isoorthology relationship with - - - - - - Orthology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - - tandem paralogous to - iterative paralogy - serial paralogy - in tandem paralogy relationship with - - - - - - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - - ISBN:978-0878932665 - - - - - - - - - - - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - - apomorphic tendency - cryptic homology - latent homologous to - underlying synapomorphy - homoiology - homoplastic tendency - re-awakening - Used for structures in closely related taxa. - in latent homology relationship with - - - - - - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - - - - ISBN:0199141118 - - - - - - - - - - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - - generative homology - syngenous to - Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. - in syngeny relationship with - - - - - - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - - DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R - - - - - - - - - - - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - - 1:1 paralogy - apparent 1:1 orthology - apparent orthologous to - pseudoorthology - The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. - in apparent orthology relationship with - - - - - - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - - - - - - - - - - - - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - - pseudoparalogous to - These genes may come out as paralogs in a single-genome analysis. - in pseudoparalogy relationship with - - - - - - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - - - - - - - - - - - - Historical homology that involves functional equivalent genes with retention of the ancestral function. - - - equivalogous to - This may include examples of orthology, paralogy and xenology. - in equivalogy relationship with - - - - - - Historical homology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - - interologous to - in interology relationship with - - - - - - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - - - - - - - - - - - - Similarity that is characterized by interchangeability in function. - - - functional similarity - in functional equivalence relationship with - - - - - - Similarity that is characterized by interchangeability in function. - - - - - - - - - - - - - Biological homology that involves parts of the same organism. - - - iterative homologous to - in iterative homology relationship with - - - - - - Biological homology that involves parts of the same organism. - - - - - - - - - - - - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - - duplicate xenology - multiple xenology - paraxenologous to - in paraxenology relationship with - - - - - - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - - - - - - - - - - - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - - plerologous to - This phenomenon is usually due to gene conversion process. - in plerology relationship with - - - - - - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - - - - - - - - - - - - Structural homology that involves structures with the same or similar relative positions. - - - homotopous to - Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. - in homotopy relationship with - - - - - - Structural homology that involves structures with the same or similar relative positions. - - - - ISBN:0123195837 - - - - - - - - - - Biological homology that involves an ectopic structure and the normally positioned structure. - - - heterotopy - in homeosis relationship with - - - - - - Biological homology that involves an ectopic structure and the normally positioned structure. - - - - - - - - - - - - - - Synology that results from allopolyploidy. - - - homoeologous to - On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. - in homoeology relationship with - - - - - - Synology that results from allopolyploidy. - - - - - - - - - - - - - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - - axis paramorphism - in paramorphism relationship with - - - - - - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - - - - - - - - - - - - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - - regulogous to - in regulogy relationship with - - - - - - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - - - - - - - - - - - - - - - - - - - - - entity - - - - - - - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - continuant - - - - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. - occurrent - - - - - - - - - - - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - - - - - A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. - obsolete dependent continuant - true - - - - - - - - - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - - - - - - disposition - - - - - - - - - - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - realizable entity - - - - - - - - - quality - - - - - - - - - - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - - - - - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - role - - - - - - - - - object aggregate - - - - - - - - - site - - - - - - - - - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - generically dependent continuant - - - - - - - - - function - - - - - - - - - - - - - - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity - - - - - - - - - - - - - - - immaterial entity - - - - - - - - - - anatomical structure - - - - - - - - - - material anatomical entity - - - - - - - - - immaterial anatomical entity - - - - - - - - - - connected anatomical system - - - - - - - - - - cell part (CARO) - cell part - - - - - - - - - - multi-cell-part structure - - - - - - - - - - neuron projection bundle - - - - - - - - - Material anatomical entity that is a member of an individual species or is a viral or viroid particle. - organism or virus - Melissa Haendel - 9/18/11 - organism or virus or viroid - - - - - - - - - - - - - - - - multicellular anatomical structure - - - - - - - - - An individual member of a clade. - organism - mah - 7.16.2011 - A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. - organism - - - - - - - - - - - - - - - - cell - - - - - - - - - - neuron - - - - - - - - - macroscopic spatial feature - geographic feature - - - - - - - - - An anthropogenic geographic feature is a geographic feature -resulting from the influence of human beings on nature. - man-made feature - manmade feature - anthropogenic geographic feature - - - - - An anthropogenic geographic feature is a geographic feature -resulting from the influence of human beings on nature. - ORCID:0000-0002-4366-3088 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A feature that has been constructed by deliberate human effort. - constructed feature - construction - - - - - A feature that has been constructed by deliberate human effort. - MA:ma - - - - - - - - - biome - - - - - - - - - An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff. - mesoscopic physical object - - - - - An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff. - MA:ma - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity which determines an environmental system. - environmental feature - - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. - manufactured good - manufactured product - - - - - A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. - https://en.wikipedia.org/wiki/Manufactured_product - - - - - - - - - anthropogenic abiotic mesoscopic feature - - - - - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - portion of environmental material - environmental material - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - DOI:10.1186/2041-1480-4-43 - MA:ma - ORCID:0000-0002-4366-3088 - URL:http://ontology.buffalo.edu/smith/articles/niches.html - - - - - - - - - abiotic mesoscopic physical object - - - - - - - - - A system which has the disposition to environ one or more material entities. - environment - environmental system - - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anthropogenic environment is an environmental system which is the product of human activity. - anthropogenic environment - - - - - - - - - Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. - space - outer space - - - - - Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. - https://en.wikipedia.org/wiki/Outer_space - - - - - - - - - A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. - human dwelling - - - - - A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. - https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 - - - - - - - - - An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. - celestial body - astronomical body - - - - - An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. - https://en.wikipedia.org/wiki/Astronomical_object - - - - - - - - - - - - - - - - - - 1 - - - - An object which is composed of one or more gravitationally bound structures that are associated with a position in space. - celestial object - astronomical object - - - - - An object which is composed of one or more gravitationally bound structures that are associated with a position in space. - https://en.wikipedia.org/wiki/Astronomical_object - - - - - - - - - - - - - - - A material part of an astronomical body. - astronomical body part - - - - - - - - - - - - - - - - A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with. - biosphere - - - - - A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with. - http://www.biology-online.org/dictionary/Biosphere - https://en.wikipedia.org/wiki/Biosphere - - - - - - - - - - - - - - - - - - - - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - natural environment - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - https://en.wikipedia.org/wiki/Anthropization - https://en.wikipedia.org/wiki/Natural_environment - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process during which a natural environmental system is altered by human action. - anthropization - anthropisation - - - - - A process during which a natural environmental system is altered by human action. - https://en.wikipedia.org/wiki/Anthropization - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body. - technosphere - - - - - An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body. - http://dx.doi.org/10.1177/2053019616677743 - http://www.yourdictionary.com/technosphere - https://www.sciencedaily.com/releases/2016/11/161130085021.htm - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. - manufacturing process - - - - - A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. - https://en.wikipedia.org/wiki/Manufacturing - - - - - - - - - - - - - - - - - - - - - - - - - - An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures. - construction process - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by materials bearing roughly homogeneous qualities. - environmental system determined by a quality - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system within which an environmental material strongly influences the system's composition and properties. - environmental system determined by a material - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by a living organism. - host-associated environment - environmental system determined by an organism - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by an animal. - animal environment - Metazoan-associated environment - animal-associated environment - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead animal, or a whole small animal. - environment associated with an animal part or small animal - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead plant, or a whole small plant. - environment associated with a plant part or small plant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which includes both living and non-living components. - ecosystem + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process - + - An environmental system which includes both living and non-living components. - https://en.wikipedia.org/wiki/Ecosystem + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + - - - - - - - - - - - - - - - - - - - A process in which includes the components of an environmental system as participants. - environmental system process - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental process which is driven by the action of humans. - anthropogenic environmental process - - - - - + - - - molecular process - molecular_function + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + - + - - - catalytic activity + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + - + - - - - - - true - - - ubiquitin-protein ligase activity + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + - + - - - receptor activity + + + object-aggregate + ObjectAggregate + a collection of cells in a blood biobank. + a swarm of bees is an aggregate of members who are linked together through natural bonds + a symphony orchestra + an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) + defined by fiat: the aggregate of members of an organization + defined through physical attachment: the aggregate of atoms in a lump of granite + defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container + defined via attributive delimitations such as: the patients in this hospital + the aggregate of bearings in a constant velocity axle joint + the aggregate of blood cells in your body + the nitrogen atoms in the atmosphere + the restaurants in Palo Alto + your collection of Meissen ceramic plates. + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + object aggregate + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + + + + + + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + + + + + + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + - + - - - - nucleus + + + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + site + + + + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + + + + + + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + - + - - - - The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. - behavioral response to stimulus - behaviour - behavioural response to stimulus - single-organism behavior - behavior + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant - + - The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. - GOC:ems - GOC:jl - ISBN:0395448956 - PMID:20160973 + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + - + - - - feeding behavior + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + - + - - - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - biological process - physiological process - single organism process - single-organism process - biological_process + + + immaterial + ImmaterialEntity + BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 + + immaterial entity - - - - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - GOC:go_curators - GOC:isa_complete - - + - - - - membrane + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + organism or virus + Melissa Haendel + 9/18/11 + organism or virus or viroid - + - - - - - - true - - - kinase activity + + + An individual member of a clade. + organism + mah + 7.16.2011 + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + organism - + - - - transferase activity + + + A feature that has been constructed by deliberate human effort. + "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference + constructed feature + construction + + + + A feature that has been constructed by deliberate human effort. + MA:ma + - + - - - transferase activity, transferring phosphorus-containing groups + + + A material entity which determines an environmental system. + ENVO + ENVO:00002297 + A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. + environmental feature + + + + A material entity which determines an environmental system. + DOI:10.1186/2041-1480-4-43 + NM:nm + ORCID:0000-0002-4366-3088 + - + - - - ligase activity + + + A system which has the disposition to environ one or more material entities. + 2013-09-23T16:04:08Z + EcoLexicon:environment + environment + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + A system which has the disposition to environ one or more material entities. + DOI:10.1186/2041-1480-4-43 + - + - - - ligase activity, forming carbon-nitrogen bonds + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. + Subclasses will be added by inference. + human dwelling + + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 + - + - - - acid-amino acid ligase activity + + + A material part of an astronomical body. + envoAstro + envoPolar + astronomical body part - + - - - small conjugating protein ligase activity + + + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. + http://orcid.org/0000-0002-4366-3088 + CMECS:577 + https://cmecscatalog.org/cmecs/classification/unit/577.html + envoCmecs + envoMarine + This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" + tidal mangrove shrubland - + - - - - axon + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + janelomax + 2012-09-20T14:06:08Z + GO:0044708 + Wikipedia:Behavior + behavioral response to stimulus + behaviour + behavioural response to stimulus + biological_process + single-organism behavior + GO:0007610 + + + + 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. +2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). + + behavior + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + GOC:ems + GOC:jl + ISBN:0395448956 + PMID:20160973 + - + - - - - dendrite + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + janelomax + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + + biological_process + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + @@ -11525,8 +1702,13 @@ resulting from the influence of human beings on nature. Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + Wikipedia:Social_behavior social behaviour + biological_process cooperative behavior + GO:0035176 + Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. + social behavior @@ -11540,60 +1722,6 @@ resulting from the influence of human beings on nature. - - - - - - - - - - - - - - - presynaptic membrane - - - - - - - - - - cell projection - - - - - - - - - - neuron projection - - - - - - - - - - - - true - - - symbiosis, encompassing mutualism through parasitism - - - - @@ -11602,6 +1730,11 @@ resulting from the influence of human beings on nature. interaction with another species interspecies interaction interspecies interaction with other organisms + biological_process + GO:0044419 + + + interspecies interaction between organisms @@ -11613,77 +1746,16 @@ resulting from the influence of human beings on nature. - - - - - - synapse part - - - - - - - - - - cell part - - - - - - - - - - synapse - - - - - - - - - - - postsynaptic membrane - - - - - - - - - - - - - - - response to stimulus - - - - - - - - - interaction with symbiont - - - - Any process in which an organism has an effect on an organism of the same species. intraspecies interaction with other organisms + biological_process + GO:0051703 + + intraspecies interaction between organisms @@ -11698,11 +1770,18 @@ resulting from the influence of human beings on nature. + A biological process which involves another organism of the same or different species. + GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism + biological_process + GO:0051704 + + + multi-organism process @@ -11720,12 +1799,18 @@ resulting from the influence of human beings on nature. Any process in which an organism has a behavioral effect on another organism of the same or different species. + GO:0023032 + GO:0044709 behavioral interaction between organisms behavioral interaction with other organism behavioural interaction between organisms behavioural interaction with other organism behavioral signaling behavioral signalling + biological_process + GO:0051705 + + multi-organism behavior @@ -11743,71 +1828,6 @@ resulting from the influence of human beings on nature. - - - - - acquisition of nutrients from other organism during symbiotic interaction - - - - - - - - - - - acquisition of nutrients from symbiont - - - - - - - - - - - - true - - - parasitism - - - - - - - - - - - - true - - - mutualism - - - - - - - - - - - - true - - - commensalism - - - - @@ -11916,35 +1936,303 @@ resulting from the influence of human beings on nature. - + - - - all - root + + + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + cjm + 2018-05-20T20:55:03Z + ontology module + + + + + + + + + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + cjm + 2018-05-20T20:55:30Z + base ontology module + + + + + + + + + + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + cjm + 2018-05-20T20:55:47Z + editors ontology module + + + + + + + + + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + cjm + 2018-05-20T20:56:13Z + main release ontology module + + + + + + + + + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + cjm + 2018-05-20T20:56:23Z + bridge ontology module + + + + + + + + + + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + cjm + 2018-05-20T20:56:47Z + import ontology module + + + + + + + + + + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + cjm + 2018-05-20T20:58:11Z + subset ontology module + + + + + + + + + + + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + cjm + 2018-05-20T20:58:38Z + curation subset ontology module + + + + + + + + + An ontology module that is intended for usage in analysis or discovery applications. + cjm + 2018-05-20T20:58:49Z + analysis subset ontology module + + + + + + + + + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + cjm + 2018-05-20T20:59:19Z + single layer subset ontology module + + + + + + + + + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + cjm + 2018-05-20T20:59:57Z + exclusion subset ontology module + + + + + + + + + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + cjm + 2018-05-20T21:00:14Z + external import ontology module + + + + + + + + + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + cjm + 2018-05-20T21:14:16Z + species subset ontology module + + + + + + + + + + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + cjm + 2018-05-20T21:20:33Z + reasoned ontology module + + + + + + + + + + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + cjm + 2018-05-20T21:21:12Z + generated ontology module + + + + + + + + + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + cjm + 2018-05-20T21:21:21Z + template generated ontology module + + + + + + + + + + + + cjm + 2018-05-20T21:28:15Z + taxonomic bridge ontology module + + + + + + + + + cjm + 2018-05-22T04:15:54Z + ontology module subsetted by expressivity + + + + + + + + + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + cjm + 2018-05-22T04:16:10Z + obo basic subset ontology module + + + + + + + + + + cjm + 2018-05-22T04:16:28Z + ontology module subsetted by OWL profile + + + + + + + + + cjm + 2018-05-22T04:16:48Z + EL++ ontology module - - - - all - - - - - - all - - - + + GC_ID:1 + ncbi_taxonomy Vira Viridae viruses + Viruses @@ -11972,6 +2260,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Teleostomi @@ -11981,7 +2272,11 @@ resulting from the influence of human beings on nature. + NCBITaxon:40673 + GC_ID:1 bony vertebrates + ncbi_taxonomy + Euteleostomi @@ -11996,9 +2291,12 @@ resulting from the influence of human beings on nature. - + + GC_ID:1 + ncbi_taxonomy Viroid viroids + Viroids @@ -12020,8 +2318,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy Charophyta/Embryophyta group charophyte/embryophyte group + Streptophytina @@ -12042,8 +2344,10 @@ resulting from the influence of human beings on nature. - + GC_ID:1 + ncbi_taxonomy biota + cellular organisms @@ -12052,12 +2356,6 @@ resulting from the influence of human beings on nature. biota - - - - biota - - @@ -12065,6 +2363,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Dipnotetrapodomorpha @@ -12074,7 +2375,12 @@ resulting from the influence of human beings on nature. + GC_ID:1 + PMID:11743200 + PMID:11791233 + ncbi_taxonomy Boreotheria + Boreoeutheria @@ -12090,6 +2396,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Acrogymnospermae @@ -12099,17 +2408,49 @@ resulting from the influence of human beings on nature. + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11542017 + PMID:11542087 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:270744 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 eubacteria + ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria - not Bacteria Haeckel 1894 prokaryote prokaryotes + Bacteria + + + + prokaryotes + + @@ -12146,24 +2487,12 @@ resulting from the influence of human beings on nature. bacteria - - - - not Bacteria Haeckel 1894 - - prokaryote - - - - prokaryotes - - @@ -12171,7 +2500,11 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy Homo/Pan/Gorilla group + Homininae @@ -12187,6 +2520,34 @@ resulting from the influence of human beings on nature. + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11541975 + PMID:11542064 + PMID:11542149 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:25527841 + PMID:270744 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 + ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria @@ -12197,6 +2558,7 @@ resulting from the influence of human beings on nature. archaea prokaryote prokaryotes + Archaea @@ -12266,13 +2628,18 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + PMID:23020233 eucaryotes eukaryotes + ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes + Eukaryota @@ -12281,84 +2648,42 @@ resulting from the influence of human beings on nature. eucaryotes - - - - eucaryotes - - eukaryotes - - - - eukaryotes - - Eucarya - - - - Eucarya - - Eucaryotae - - - - Eucaryotae - - Eukarya - - - - Eukarya - - Eukaryotae - - - - Eukaryotae - - eukaryotes - - - - eukaryotes - - @@ -12366,11 +2691,16 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + PMID:23020233 green algae + ncbi_taxonomy Chlorophycota Chlorophyta sensu Bremer 1985 algae green algae + Chlorophyta @@ -12410,6 +2740,14 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + PMID:11214319 + PMID:12082125 + PMID:12878460 + PMID:15522813 + ncbi_taxonomy + Euarchontoglires @@ -12419,7 +2757,11 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy Anthropoidea + Simiiformes @@ -12435,8 +2777,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 ape apes + ncbi_taxonomy + Hominoidea @@ -12458,10 +2804,13 @@ resulting from the influence of human beings on nature. + GC_ID:1 higher plants land plants plants + ncbi_taxonomy land plants + Embryophyta @@ -12495,7 +2844,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 tetrapods + ncbi_taxonomy + Tetrapoda @@ -12511,7 +2863,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 amniotes + ncbi_taxonomy + Amniota @@ -12527,7 +2882,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 Theria + ncbi_taxonomy + Theria <Mammalia> @@ -12543,11 +2901,15 @@ resulting from the influence of human beings on nature. + + GC_ID:1 green plants + ncbi_taxonomy Chlorobionta Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants + Viridiplantae @@ -12587,8 +2949,11 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy Fungi/Metazoa group opisthokonts + Opisthokonta @@ -12610,10 +2975,14 @@ resulting from the influence of human beings on nature. + + GC_ID:1 metazoans multicellular animals + ncbi_taxonomy Animalia animals + Metazoa @@ -12647,6 +3016,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Bilateria @@ -12656,7 +3028,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 deuterostomes + ncbi_taxonomy + Deuterostomia @@ -12672,10 +3047,14 @@ resulting from the influence of human beings on nature. + GC_ID:1 + PMID:25249442 angiosperms flowering plants + ncbi_taxonomy Angiospermae flowering plants + Magnoliophyta @@ -12709,6 +3088,10 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy + Streptophyta @@ -12718,6 +3101,10 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy + Haplorrhini @@ -12727,8 +3114,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 mammals + ncbi_taxonomy mammals + Mammalia @@ -12750,8 +3141,11 @@ resulting from the influence of human beings on nature. + GC_ID:1 vascular plants + ncbi_taxonomy vascular plants + Tracheophyta @@ -12773,8 +3167,11 @@ resulting from the influence of human beings on nature. + GC_ID:1 seed plants + ncbi_taxonomy seed plants + Spermatophyta @@ -12796,6 +3193,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Eumetazoa @@ -12805,8 +3205,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 chordates + ncbi_taxonomy chordates + Chordata @@ -12828,9 +3232,12 @@ resulting from the influence of human beings on nature. + GC_ID:1 Vertebrata vertebrates + ncbi_taxonomy vertebrates + Vertebrata <Metazoa> @@ -12858,8 +3265,11 @@ resulting from the influence of human beings on nature. + GC_ID:1 Gnathostomata jawed vertebrates + ncbi_taxonomy + Gnathostomata <vertebrate> @@ -12881,7 +3291,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy euphyllophytes + Euphyllophyta @@ -12897,6 +3310,10 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy + Sarcopterygii @@ -12906,7 +3323,11 @@ resulting from the influence of human beings on nature. + + GC_ID:1 Craniata + ncbi_taxonomy + Craniata <chordata> @@ -12922,11 +3343,14 @@ resulting from the influence of human beings on nature. + GC_ID:1 eutherian mammals placental mammals placentals + ncbi_taxonomy Placentalia placentals + Eutheria @@ -12966,9 +3390,13 @@ resulting from the influence of human beings on nature. + + GC_ID:1 primate + ncbi_taxonomy Primata primates + Primates @@ -12996,6 +3424,10 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy + Catarrhini @@ -13005,8 +3437,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 great apes + ncbi_taxonomy Pongidae + Hominidae @@ -13028,7 +3464,11 @@ resulting from the influence of human beings on nature. + + GC_ID:1 humans + ncbi_taxonomy + Homo @@ -13044,9 +3484,25 @@ resulting from the influence of human beings on nature. + + GC_ID:1 human man - humans + ncbi_taxonomy + Home sapiens + Homo sampiens + Homo sapeins + Homo sapian + Homo sapians + Homo sapien + Homo sapience + Homo sapiense + Homo sapients + Homo sapines + Homo spaiens + Homo spiens + Humo sapiens + Homo sapiens @@ -13061,16 +3517,96 @@ resulting from the influence of human beings on nature. man + + + + Home sapiens + + + + + + Homo sampiens + + + + + + Homo sapeins + + + + + + Homo sapian + + + + + + Homo sapians + + + + + + Homo sapien + + + + + + Homo sapience + + + + + + Homo sapiense + + + + + + Homo sapients + + + + + + Homo sapines + + + + + + Homo spaiens + + + + + + Homo spiens + + + + + + Humo sapiens + + - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - quality (PATO) + PATO:0000072 trait + quality + PATO:0000001 + quality @@ -13082,87 +3618,16 @@ resulting from the influence of human beings on nature. - - - - - A composite chromatic quality composed of hue, saturation and intensity parts. - colour - relative color - color - - - - - A composite chromatic quality composed of hue, saturation and intensity parts. - PATOC:GVG - - - - - - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - morphology - - - - - - - - - shape - - - - - - - - - qualitative - - - - - - - - - A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. - deviation(from_normal) - - - - - - - - - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. - size - - - - - - - - - structure - - - - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + rate @@ -13174,82 +3639,21 @@ resulting from the influence of human beings on nature. - - - - - A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers. - red - - - - - A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers. - Dictionary:http://dictionary.reference.com/ - - - - - - - - - branched - - - - - - - - - - A size quality which is relatively low. - hypoplasia - underdeveloped - reduced - small - tiny - decreased size - - - - - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - relational physical quality - physical quality - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATOC:GVG - - - - - - - - - linear - - - - A quality which inheres in an process. + PATO:0001239 + PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent + quality + PATO:0001236 + See comments of relational quality of a physical entity. + process quality @@ -13266,6 +3670,9 @@ resulting from the influence of human beings on nature. A quality which inheres in a continuant. + PATO:0001237 + PATO:0001238 + snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant @@ -13274,6 +3681,10 @@ resulting from the influence of human beings on nature. quality of continuant monadic quality of an object monadic quality of continuant + quality + PATO:0001241 + Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. + physical object quality @@ -13285,43 +3696,16 @@ resulting from the influence of human beings on nature. - - - - - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - electromagnetic (EM) radiation quality - - - - - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation - - - - - - - - - An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. - optical quality - - - - - An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. - PATOC:GVG - - - - A biological sex quality inhering in a population of multiple sexes. + quality + PATO:0001338 + + For example a mixture of females and male or males and hermaphrodites. + mixed sex @@ -13338,6 +3722,11 @@ resulting from the influence of human beings on nature. A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. + quality + PATO:0001415 + + + morbidity @@ -13349,27 +3738,15 @@ resulting from the influence of human beings on nature. - - - - - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. - radiation quality - - - - - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. - PATOC:GVG - - - - A quality that inheres in an entire population or part of a population. + quality + PATO:0002003 + + population quality @@ -13381,54 +3758,21 @@ resulting from the influence of human beings on nature. - - - - - branchiness - - - - + george + 2009-06-05T09:16:46Z + quality + PATO:0002062 + + physical quality of a process - - - - - laminar - - - - - - - - - A quality that has a value that is decreased compared to normal or average. - decreased quality - - - - - - - - - - A quality of an object that has a value that is decreased compared to normal or average. - decreased object quality - - - - @@ -13458,12 +3802,10 @@ resulting from the influence of human beings on nature. Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. - A material entity that consists of two or more organisms, viruses, or viroids. group of organism organism collection May be of the same or different species. collection of organisms - collection of organisms @@ -13477,7 +3819,7 @@ resulting from the influence of human beings on nature. A collection of organisms, all of the same species, that live in the same place. ISBN:0878932739 - It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. + It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. population of organisms @@ -13488,49 +3830,19 @@ Classes for population already exist in IDO ('organism population', I - + - + 2 - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - A community of at least two different species, living in a particular area. Must have at least two populations of different species as members. - Not sure if the equivalancy axiom specifies that both populations are located in the same site. + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. @@ -13870,16 +4182,14 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - A material entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. - + + + + + + + + An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. Person: Jie Zheng WEB: http://en.wikipedia.org/wiki/Household household @@ -13949,12 +4259,13 @@ Classes for population already exist in IDO ('organism population', I - - + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. + These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). community + true @@ -13996,7 +4307,7 @@ Classes for population already exist in IDO ('organism population', I - + A material entity that is one or more organisms, viruses or viroids. organismal entity @@ -14096,7 +4407,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -14110,6 +4421,7 @@ Classes for population already exist in IDO ('organism population', I + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. pair of interacting organisms @@ -14135,6 +4447,7 @@ Classes for population already exist in IDO ('organism population', I + pair of interacting organisms of the same species @@ -14212,220 +4525,228 @@ Classes for population already exist in IDO ('organism population', I - + + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 http://orcid.org/0000-0002-4366-3088 http://dx.doi.org/10.1038/ismej.2009.88 + microbiota The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. microbial community - - - - - A plant structure (PO:0005679) which is a whole organism. - genet (broad) - ramet (broad) - planta entera (Spanish, exact) - 植物体全体 (Japanese, exact) - bush (narrow) - frutex (narrow) - frutices (narrow) - gametophyte (narrow) - herb (narrow) - liana (narrow) - prothalli (narrow) - prothallium (narrow) - prothallus (narrow) - seedling (narrow) - shrub (narrow) - sporophyte (narrow) - suffrutex (narrow) - suffrutices (narrow) - tree (narrow) - vine (narrow) - woody clump (narrow) - clonal colony (related) - colony (related) - whole plant - - - - - + - - - An anatomical structure that is or was part of a plant, or was derived from a part of a plant. - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) - plant structure + + + A material entity that is one or more organisms, viruses or viroids. + wrong IRI form + http://purl.obolibrary.org/obo/PCO_0000031 + obsolete organismal entity + true - + - - - An anatomical entity that is or was part of a plant. - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) - plant anatomical entity + + - + - - - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, - An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. - This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. - Chris Mungall - cjm - 2017-06-05T17:55:39Z - exposure event or process - https://github.com/oborel/obo-relations/pull/173 + + - + - - - - - - - - - Any entity that is ordered in discrete units along a linear axis. - Chris Mungall - sequentially ordered entity - + - + - - - Any individual unit of a collection of like units arranged in a linear order - Chris Mungall - An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. - sequence atomic unit + + + + + + + + + - + - - - Any entity that can be divided into parts such that each part is an atomical unit of a sequence - Chris Mungall - Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. - sequence bearer + + - + - - - A material entity consisting of multiple components that are causally integrated. - May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 - Chris Mungall - http://www.jbiomedsem.com/content/4/1/43 - system + + - + - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - anatomical entity + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community - + - - - A material entity that is one or more organisms, viruses or viroids. - wrong IRI form - http://purl.obolibrary.org/obo/PCO_0000031 - obsolete organismal entity - true + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye - + - - + + + + + + + + + microbial organism + microbe - + - - + + + + + + + + + + + 2 + + + + + + + + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms - + - - - Obsolete Class + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes - + - + - - - + + + + + + + + + + + 1 + + + + + + + 2 + + + - - - - - - - - - + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes - + - - + + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population @@ -14485,7 +4806,6 @@ Classes for population already exist in IDO ('organism population', I - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -14516,7 +4836,6 @@ Classes for population already exist in IDO ('organism population', I - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -14626,7 +4945,6 @@ Classes for population already exist in IDO ('organism population', I - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI @@ -14635,75 +4953,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - -## Elucidation - -This is used when the statement/axiom is assumed to hold true 'eternally' - -## How to interpret (informal) - -First the "atemporal" FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. - -## Example - - Class: nucleus - SubClassOf: part_of some cell - - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) - -## Notes - -This interpretation is *not* the same as an at-all-times relation - - - axiom holds for all times - - - - - - - - - -## Elucidation - -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. - -## Example: - - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm - - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - - - - relation has no temporal argument - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -14775,957 +4983,9 @@ binary, and takes no temporal argument. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z - contrib to MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From ligand activity to has_ligand - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From has_ligand to ligand activity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff --git a/reports/pco-edit.owl-obo-report.tsv b/reports/pco-edit.owl-obo-report.tsv new file mode 100644 index 0000000..4d1219e --- /dev/null +++ b/reports/pco-edit.owl-obo-report.tsv @@ -0,0 +1,24 @@ +Level Rule Name Subject Property Value +ERROR missing_label GO:0051704 rdfs:label +ERROR missing_label IAO:0000030 rdfs:label +ERROR missing_ontology_description pco.owl dc11:description +ERROR missing_ontology_license pco.owl dc:license +ERROR missing_ontology_title pco.owl dc11:title +WARN missing_definition GO:0051704 IAO:0000115 +WARN missing_definition IAO:0000030 IAO:0000115 +WARN missing_definition PCO:0000006 IAO:0000115 +WARN missing_definition PCO:0000007 IAO:0000115 +WARN missing_definition PCO:0000008 IAO:0000115 +WARN missing_definition PCO:0000014 IAO:0000115 +WARN missing_definition PCO:0000015 IAO:0000115 +WARN missing_definition PCO:0000016 IAO:0000115 +WARN missing_definition PCO:0000037 IAO:0000115 +WARN missing_definition PCO:0001001 IAO:0000115 +WARN missing_definition https://purl.obolibrary.org/obo/PCO_0000042 IAO:0000115 +WARN missing_obsolete_label PCO:0000025 rdfs:label red population@en +WARN missing_obsolete_label PCO:0000026 rdfs:label red organism@en +WARN missing_obsolete_label PCO:0000028 rdfs:label community@en +INFO missing_superclass PCO:0000003 rdfs:subClassOf +INFO missing_superclass PCO:0000004 rdfs:subClassOf +INFO missing_superclass https://purl.obolibrary.org/obo/PCO_0000043 rdfs:subClassOf +INFO missing_superclass https://purl.obolibrary.org/obo/PCO_0000045 rdfs:subClassOf diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 40df2ad..db3aa85 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -43,7 +43,7 @@ RELEASE_ARTEFACTS = $(sort full base base full) .PHONY: .FORCE all: odkversion all_imports all_main all_subsets sparql_test all_reports all_assets test: odkversion sparql_test all_reports - $(ROBOT) reason --input $(SRC) --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural --output test.owl && rm test.owl && echo "Success" + $(ROBOT) reason --input $(SRC) --reasoner hermit --equivalent-classes-allowed all --exclude-tautologies structural --output test.owl && rm test.owl && echo "Success" odkversion: echo "ODK Makefile version: $(ODK_VERSION) (this is the version of the ODK with which this Makefile was generated, not the version of the ODK you are running)" &&\ @@ -77,7 +77,7 @@ all_imports: $(IMPORT_FILES) all_imports_owl: $(foreach n,$(IMPORT_ROOTS), $(n).owl) -all_imports_obo: $(foreach n,$(IMPORT_ROOTS), $(n).obo) +# all_imports_obo: $(foreach n,$(IMPORT_ROOTS), $(n).obo) ## -- subset targets -- @@ -194,9 +194,9 @@ $(ONT)-base.owl: $(SRC) $(OTHER_SRC) # Full: The full artefacts with imports merged, reasoned $(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(ROBOT) merge --input $< \ - reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \ + reason --reasoner hermit --equivalent-classes-allowed all --exclude-tautologies structural \ relax \ - reduce -r ELK \ + reduce -r hermit \ annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output $@.tmp.owl && mv $@.tmp.owl $@ # ---------------------------------------- @@ -239,8 +239,8 @@ imports/%_import.obo: imports/%_import.owl # ---------------------------------------- # -IMP=true # Global parameter to bypass import generation -MIR=true # Global parameter to bypass mirror generation +IMP=false # Global parameter to bypass import generation +MIR=false # Global parameter to bypass mirror generation ## ONTOLOGY: bfo diff --git a/src/ontology/imports/envo_import.obo b/src/ontology/imports/envo_import.obo new file mode 100644 index 0000000..0e05ab0 --- /dev/null +++ b/src/ontology/imports/envo_import.obo @@ -0,0 +1,71 @@ +format-version: 1.2 +default-namespace: ENVO +remark: ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. \n\nNew terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ \n\n\nPlease see www.environmentontology.org for more information and citations. +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 186 Logical Axioms: 30] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 114 Logical Axioms: 19] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 132 Logical Axioms: 23] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 40 Logical Axioms: 6] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 21 Logical Axioms: 2] +ontology: pco/imports/envo_import +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-6601-2165 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8343-612X xsd:string +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0003-1604-1512 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0002-6962-2807 xsd:string + +[Term] +id: ENVO:00000070 +name: construction +def: "A feature that has been constructed by deliberate human effort." [MA:ma] +synonym: "constructed feature" EXACT [] +is_a: BFO:0000040 +is_a: ENVO:00002297 ! environmental feature +is_a: ENVO:01000813 ! astronomical body part +property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string + +[Term] +id: ENVO:00002297 +name: environmental feature +def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] +comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. +is_a: BFO:0000040 + +[Term] +id: ENVO:01000254 +name: environmental system +def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +synonym: "environment" EXACT [] +xref: EcoLexicon:environment +is_a: BFO:0000040 +creation_date: 2013-09-23T16:04:08Z + +[Term] +id: ENVO:01000744 +name: human dwelling +def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] +is_a: ENVO:00000070 ! construction +property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string + +[Term] +id: ENVO:01000813 +name: astronomical body part +def: "A material part of an astronomical body." [] +subset: envoAstro +subset: envoPolar +is_a: BFO:0000040 +is_a: ENVO:00002297 ! environmental feature + +[Term] +id: ENVO:01001369 +name: tidal mangrove shrubland +alt_id: CMECS:577 +def: "A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas." [] +comment: This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" +subset: envoCmecs +subset: envoMarine +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ENVO:01000254 ! environmental system +created_by: http://orcid.org/0000-0002-4366-3088 + diff --git a/src/ontology/imports/go_import.obo b/src/ontology/imports/go_import.obo new file mode 100644 index 0000000..6c1fbb0 --- /dev/null +++ b/src/ontology/imports/go_import.obo @@ -0,0 +1,118 @@ +format-version: 1.2 +ontology: pco/imports/go_import + +[Term] +id: GO:0007610 +name: behavior +namespace: biological_process +alt_id: GO:0044708 +def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] +comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). +subset: gocheck_do_not_manually_annotate +subset: goslim_agr +subset: goslim_flybase_ribbon +synonym: "behavioral response to stimulus" EXACT [] +synonym: "behaviour" EXACT [] +synonym: "behavioural response to stimulus" EXACT [] +synonym: "single-organism behavior" RELATED [] +xref: Wikipedia:Behavior +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-20T14:06:08Z + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0035176 +name: social behavior +namespace: biological_process +def: "Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group." [GOC:jh2, PMID:12848939, Wikipedia:Social_behavior] +comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. +synonym: "cooperative behavior" RELATED [] +synonym: "social behaviour" EXACT [] +xref: Wikipedia:Social_behavior +is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051705 ! multi-organism behavior +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0044419 +name: interspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +subset: goslim_candida +subset: goslim_pir +synonym: "interaction with another species" EXACT [] +synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051703 +name: intraspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: goslim_pir +synonym: "intraspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051704 +name: multi-organism process +namespace: biological_process +alt_id: GO:0051706 +def: "A biological process which involves another organism of the same or different species." [GOC:jl] +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "interaction between organisms" EXACT [] +synonym: "physiological interaction between organisms" EXACT [] +synonym: "physiological interaction with other organism" EXACT [] +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051705 +name: multi-organism behavior +namespace: biological_process +alt_id: GO:0023032 +alt_id: GO:0044709 +def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] +subset: goslim_pir +synonym: "behavioral interaction between organisms" EXACT [] +synonym: "behavioral interaction with other organism" EXACT [] +synonym: "behavioral signaling" NARROW [] +synonym: "behavioral signalling" NARROW [GOC:mah] +synonym: "behavioural interaction between organisms" EXACT [] +synonym: "behavioural interaction with other organism" EXACT [] +is_a: GO:0007610 ! behavior +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + diff --git a/src/ontology/imports/ncbitaxon_import.obo b/src/ontology/imports/ncbitaxon_import.obo new file mode 100644 index 0000000..3ba2b8c --- /dev/null +++ b/src/ontology/imports/ncbitaxon_import.obo @@ -0,0 +1,550 @@ +format-version: 1.2 +ontology: pco/imports/ncbitaxon_import + +[Term] +id: NCBITaxon:10239 +name: Viruses +namespace: ncbi_taxonomy +synonym: "Vira" RELATED synonym [] +synonym: "Viridae" RELATED synonym [] +synonym: "viruses" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117570 +name: Teleostomi +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:7776 ! Gnathostomata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117571 +name: Euteleostomi +namespace: ncbi_taxonomy +alt_id: NCBITaxon:40673 +synonym: "bony vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:117570 ! Teleostomi +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:12884 +name: Viroids +namespace: ncbi_taxonomy +synonym: "Viroid" RELATED synonym [] +synonym: "viroids" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131221 +name: Streptophytina +namespace: ncbi_taxonomy +synonym: "Charophyta/Embryophyta group" RELATED synonym [] +synonym: "charophyte/embryophyte group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:35493 ! Streptophyta +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131567 +name: cellular organisms +namespace: ncbi_taxonomy +synonym: "biota" RELATED synonym [] +xref: GC_ID:1 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1338369 +name: Dipnotetrapodomorpha +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:8287 ! Sarcopterygii +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437010 +name: Boreoeutheria +namespace: ncbi_taxonomy +synonym: "Boreotheria" RELATED synonym [] +xref: GC_ID:1 +xref: PMID:11743200 +xref: PMID:11791233 +is_a: NCBITaxon:9347 ! Eutheria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437180 +name: Acrogymnospermae +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2 +name: Bacteria +namespace: ncbi_taxonomy +synonym: "bacteria" RELATED blast_name [] +synonym: "eubacteria" EXACT genbank_common_name [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11542017 +xref: PMID:11542087 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:207598 +name: Homininae +namespace: ncbi_taxonomy +synonym: "Homo/Pan/Gorilla group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:9604 ! Hominidae +property_value: has_rank NCBITaxon:subfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2157 +name: Archaea +namespace: ncbi_taxonomy +synonym: "archaea" RELATED blast_name [] +synonym: "Archaebacteria" RELATED synonym [] +synonym: "Mendosicutes" RELATED synonym [] +synonym: "Metabacteria" RELATED synonym [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11541975 +xref: PMID:11542064 +xref: PMID:11542149 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:25527841 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2759 +name: Eukaryota +namespace: ncbi_taxonomy +synonym: "Eucarya" RELATED synonym [] +synonym: "Eucaryotae" RELATED synonym [] +synonym: "eucaryotes" EXACT genbank_common_name [] +synonym: "Eukarya" RELATED synonym [] +synonym: "Eukaryotae" RELATED synonym [] +synonym: "eukaryotes" EXACT common_name [] +synonym: "eukaryotes" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3041 +name: Chlorophyta +namespace: ncbi_taxonomy +synonym: "algae" RELATED in_part [] +synonym: "Chlorophycota" RELATED synonym [] +synonym: "Chlorophyta sensu Bremer 1985" RELATED synonym [] +synonym: "green algae" EXACT genbank_common_name [] +synonym: "green algae" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314146 +name: Euarchontoglires +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:11214319 +xref: PMID:12082125 +xref: PMID:12878460 +xref: PMID:15522813 +is_a: NCBITaxon:1437010 ! Boreoeutheria +property_value: has_rank NCBITaxon:superorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314293 +name: Simiiformes +namespace: ncbi_taxonomy +synonym: "Anthropoidea" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:376913 ! Haplorrhini +property_value: has_rank NCBITaxon:infraorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314295 +name: Hominoidea +namespace: ncbi_taxonomy +synonym: "ape" EXACT common_name [] +synonym: "apes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9526 ! Catarrhini +property_value: has_rank NCBITaxon:superfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3193 +name: Embryophyta +namespace: ncbi_taxonomy +synonym: "higher plants" EXACT common_name [] +synonym: "land plants" EXACT common_name [] +synonym: "land plants" RELATED blast_name [] +synonym: "plants" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:131221 ! Streptophytina +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32523 +name: Tetrapoda +namespace: ncbi_taxonomy +synonym: "tetrapods" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32524 +name: Amniota +namespace: ncbi_taxonomy +synonym: "amniotes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32523 ! Tetrapoda +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32525 +name: Theria +namespace: ncbi_taxonomy +synonym: "Theria" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:40674 ! Mammalia +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33090 +name: Viridiplantae +namespace: ncbi_taxonomy +synonym: "Chlorobionta" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] +synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "green plants" EXACT common_name [] +synonym: "green plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33154 +name: Opisthokonta +namespace: ncbi_taxonomy +synonym: "Fungi/Metazoa group" RELATED synonym [] +synonym: "opisthokonts" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33208 +name: Metazoa +namespace: ncbi_taxonomy +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33213 +name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:6072 ! Eumetazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33511 +name: Deuterostomia +namespace: ncbi_taxonomy +synonym: "deuterostomes" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33213 ! Bilateria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3398 +name: Magnoliophyta +namespace: ncbi_taxonomy +synonym: "Angiospermae" RELATED synonym [] +synonym: "angiosperms" EXACT common_name [] +synonym: "flowering plants" EXACT genbank_common_name [] +synonym: "flowering plants" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:25249442 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:35493 +name: Streptophyta +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:376913 +name: Haplorrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:9443 ! Primates +property_value: has_rank NCBITaxon:suborder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:40674 +name: Mammalia +namespace: ncbi_taxonomy +synonym: "mammals" EXACT genbank_common_name [] +synonym: "mammals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32524 ! Amniota +property_value: has_rank NCBITaxon:class +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58023 +name: Tracheophyta +namespace: ncbi_taxonomy +synonym: "vascular plants" EXACT common_name [] +synonym: "vascular plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:3193 ! Embryophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58024 +name: Spermatophyta +namespace: ncbi_taxonomy +synonym: "seed plants" EXACT common_name [] +synonym: "seed plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:78536 ! Euphyllophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33208 ! Metazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7711 +name: Chordata +namespace: ncbi_taxonomy +synonym: "chordates" EXACT genbank_common_name [] +synonym: "chordates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33511 ! Deuterostomia +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7742 +name: Vertebrata +namespace: ncbi_taxonomy +synonym: "Vertebrata" EXACT scientific_name [] +synonym: "vertebrates" EXACT genbank_common_name [] +synonym: "vertebrates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:89593 ! Craniata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7776 +name: Gnathostomata +namespace: ncbi_taxonomy +synonym: "Gnathostomata" EXACT scientific_name [] +synonym: "jawed vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7742 ! Vertebrata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:78536 +name: Euphyllophyta +namespace: ncbi_taxonomy +synonym: "euphyllophytes" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:58023 ! Tracheophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:8287 +name: Sarcopterygii +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:117571 ! Euteleostomi +property_value: has_rank NCBITaxon:superclass +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:89593 +name: Craniata +namespace: ncbi_taxonomy +synonym: "Craniata" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7711 ! Chordata +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9347 +name: Eutheria +namespace: ncbi_taxonomy +synonym: "eutherian mammals" EXACT common_name [] +synonym: "placental mammals" EXACT common_name [] +synonym: "Placentalia" RELATED synonym [] +synonym: "placentals" EXACT genbank_common_name [] +synonym: "placentals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32525 ! Theria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9443 +name: Primates +namespace: ncbi_taxonomy +synonym: "Primata" RELATED synonym [] +synonym: "primate" EXACT equivalent_name [] +synonym: "primates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:314146 ! Euarchontoglires +property_value: has_rank NCBITaxon:order +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9526 +name: Catarrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:314293 ! Simiiformes +property_value: has_rank NCBITaxon:parvorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9604 +name: Hominidae +namespace: ncbi_taxonomy +synonym: "great apes" EXACT genbank_common_name [] +synonym: "Pongidae" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:314295 ! Hominoidea +property_value: has_rank NCBITaxon:family +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9605 +name: Homo +namespace: ncbi_taxonomy +synonym: "humans" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:207598 ! Homininae +property_value: has_rank NCBITaxon:genus +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9606 +name: Homo sapiens +namespace: ncbi_taxonomy +synonym: "Home sapiens" RELATED misspelling [] +synonym: "Homo sampiens" RELATED misspelling [] +synonym: "Homo sapeins" RELATED misspelling [] +synonym: "Homo sapian" RELATED misspelling [] +synonym: "Homo sapians" RELATED misspelling [] +synonym: "Homo sapien" RELATED misspelling [] +synonym: "Homo sapience" RELATED misspelling [] +synonym: "Homo sapiense" RELATED misspelling [] +synonym: "Homo sapients" RELATED misspelling [] +synonym: "Homo sapines" RELATED misspelling [] +synonym: "Homo spaiens" RELATED misspelling [] +synonym: "Homo spiens" RELATED misspelling [] +synonym: "human" EXACT genbank_common_name [] +synonym: "Humo sapiens" RELATED misspelling [] +synonym: "man" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9605 ! Homo +property_value: has_rank NCBITaxon:species +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + diff --git a/src/ontology/imports/pato_import.obo b/src/ontology/imports/pato_import.obo new file mode 100644 index 0000000..8c8a22f --- /dev/null +++ b/src/ontology/imports/pato_import.obo @@ -0,0 +1,96 @@ +format-version: 1.2 +ontology: pco/imports/pato_import + +[Term] +id: PATO:0000001 +name: quality +namespace: quality +alt_id: PATO:0000072 +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +synonym: "trait" EXACT [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000161 +name: rate +namespace: quality +def: "A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time." [PATOC:melissa] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002062 ! physical quality of a process +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001236 +name: process quality +namespace: quality +alt_id: PATO:0001239 +alt_id: PATO:0001240 +def: "A quality which inheres in an process." [PATOC:GVG] +comment: See comments of relational quality of a physical entity. +synonym: "quality of a process" EXACT [] +synonym: "quality of occurrent" EXACT [] +synonym: "quality of process" EXACT [] +synonym: "relational quality of occurrent" EXACT [] +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001241 +name: physical object quality +namespace: quality +alt_id: PATO:0001237 +alt_id: PATO:0001238 +def: "A quality which inheres in a continuant." [PATOC:GVG] +comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. +synonym: "monadic quality of a continuant" EXACT [] +synonym: "monadic quality of an object" NARROW [] +synonym: "monadic quality of continuant" NARROW [] +synonym: "multiply inhering quality of a physical entity" EXACT [] +synonym: "quality of a continuant" EXACT [] +synonym: "quality of a single physical entity" EXACT [] +synonym: "quality of an object" EXACT [] +synonym: "quality of continuant" EXACT [] +xref: snap:Quality +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001338 +name: mixed sex +namespace: quality +def: "A biological sex quality inhering in a population of multiple sexes." [MGED:MGED] +comment: For example a mixture of females and male or males and hermaphrodites. +subset: value_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001415 +name: morbidity +namespace: quality +def: "A quality inhering in a population by virtue of the proportion of its members that are ill at a given time." [PATOC:GVG] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002003 +name: population quality +namespace: quality +def: "A quality that inheres in an entire population or part of a population." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002062 +name: physical quality of a process +namespace: quality +subset: attribute_slim +is_a: PATO:0001236 ! process quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +created_by: george +creation_date: 2009-06-05T09:16:46Z + diff --git a/src/ontology/pco-base.obo b/src/ontology/pco-base.obo new file mode 100644 index 0000000..1c082c0 --- /dev/null +++ b/src/ontology/pco-base.obo @@ -0,0 +1,493 @@ +format-version: 1.2 +data-version: pco/releases/2020-02-13/pco-base.owl +remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. +ontology: pco/pco-base +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string +property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string +property_value: http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 xsd:string + +[Term] +id: CARO:0001010 +name: organism or virus or viroid +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +is_a: BFO:0000040 +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "organism or virus" xsd:string + +[Term] +id: CARO:0010004 +name: organism +def: "An individual member of a clade." [] +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +is_a: CARO:0001010 ! organism or virus or viroid +property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string +property_value: IAO:0000589 "organism" xsd:string + +[Term] +id: GO:0051704 +is_a: BFO:0000015 + +[Term] +id: IAO:0000030 +is_a: BFO:0000031 + +[Term] +id: PCO:0000000 +name: collection of organisms +def: "A material entity that consists of two or more organisms, viruses, or viroids." [] +comment: May be of the same or different species. +is_a: BFO:0000027 +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid +property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "group of organism" xsd:string +property_value: IAO:0000118 "organism collection" xsd:string + +[Term] +id: PCO:0000001 +name: population of organisms +def: "A collection of organisms, all of the same species, that live in the same place." [] +comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000112 "" xsd:string +property_value: IAO:0000112 "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 ISBN:0878932739 xsd:string + +[Term] +id: PCO:0000002 +name: ecological community +def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] +comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +property_value: IAO:0000118 "multispecies community" xsd:string +property_value: IAO:0000119 ISBN:0865423504 xsd:string + +[Term] +id: PCO:0000003 +name: quality of a population +def: "A quality that inheres in a biological population." [] +comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. +intersection_of: PATO:0002003 +intersection_of: RO:0000052 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000004 +name: quality of an ecological community +def: "A quality that inheres in a community." [] +comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. +intersection_of: PATO:0002003 +intersection_of: RO:0000052 PCO:0000002 ! ecological community +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000005 +name: population process +def: "A process that has as primary participant a population. " [] +comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +is_a: BFO:0000015 +relationship: RO:0000057 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000006 +name: population birth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000007 +name: population death rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000008 +name: population growth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string + +[Term] +id: PCO:0000009 +name: obsolete carrying capacity +def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] +is_a: ObsoleteClass +property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +property_value: IAO:0000119 ISBN:0878932739 xsd:string +property_value: IAO:0000231 IAO:0000423 +is_obsolete: true + +[Term] +id: PCO:0000010 +name: community species richness +def: "The number of different species represented in an ecological community." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string + +[Term] +id: PCO:0000011 +name: population growth +def: "A process that leads to a change in the number of individuals (positive or negative) in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000012 +name: logistic population growth +def: "A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000013 +name: exponential population growth +def: "A population growth process that leads to an exponential increase in the number of individuals in a population." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000014 +name: predator role +is_a: BFO:0000023 +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000015 +name: prey role +is_a: BFO:0000023 +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000016 +name: symbiont role +is_a: BFO:0000023 +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000017 +name: species as a collection of organisms +def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string + +[Term] +id: PCO:0000018 +name: single-species collection of organisms +def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000118 "collection of organisms of the same species" xsd:string + +[Term] +id: PCO:0000019 +name: community species diversity +def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] +comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string + +[Term] +id: PCO:0000020 +name: family +def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] +comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string +property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string + +[Term] +id: PCO:0000021 +name: population extinction +def: "A population process that ultimately leads to the death of all individuals in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000022 +name: species extinction +def: "A process that ultimately leads to the death of all individuals in a population." [] +is_a: BFO:0000015 +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000023 +name: community species evenness +def: "A quality of a community that reflects how close in abundance all species in a community are." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_evenness" xsd:string + +[Term] +id: PCO:0000024 +name: household +def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] +is_a: PCO:0000031 ! organismal entity +relationship: RO:0002321 ENVO:01000744 +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string + +[Term] +id: PCO:0000025 +name: red population +comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000026 +name: red organism +comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000027 +name: collection of humans +def: "A collection of organisms of the same species that has as members only humans." [] +is_a: PCO:0000018 ! single-species collection of organisms +intersection_of: PCO:0000018 ! single-species collection of organisms +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "human community" xsd:string +property_value: IAO:0000118 "human population" xsd:string + +[Term] +id: PCO:0000028 +name: community +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). +is_a: ObsoleteClass +property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000029 +name: multi-species collection of organisms +def: "A collection of organisms that consists of two or more organisms from at least two species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string + +[Term] +id: PCO:0000030 +name: agricultural household +name: obsolete organismal entity +def: "A household in which the majority of the income of its members is derived from agricultural activities." [] +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: ObsoleteClass +is_a: PCO:0000024 ! household +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string +property_value: IAO:0000231 "wrong IRI form" xsd:string +is_obsolete: true +replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 + +[Term] +id: PCO:0000031 +name: organismal entity +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: BFO:0000040 +union_of: CARO:0001010 ! organism or virus or viroid +union_of: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 + +[Term] +id: PCO:0000032 +name: biological family +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +is_a: PCO:0000020 ! family +property_value: IAO:0000118 "genealogical family" xsd:string +property_value: IAO:0000119 "Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/" xsd:string + +[Term] +id: PCO:0000033 +name: human social gathering activity +def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] +is_a: GO:0035176 +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000034 +name: human community event +def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000035 +name: party +def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000037 +name: potluck +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string +property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000038 +name: wedding +def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000039 +name: baby shower +def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000040 +name: tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: PCO:0000002 ! ecological community +relationship: BFO:0000050 ENVO:01001369 +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string + +[Term] +id: PCO:0000041 +name: invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: PATO:0001241 + +[Term] +id: PCO:0000042 +name: microbe +synonym: "microbial organism" EXACT [] +is_a: CARO:0001010 ! organism or virus or viroid +relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye + +[Term] +id: PCO:0000043 +name: collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe +intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000044 +name: multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: PCO:0000029 ! multi-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000045 +name: single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000046 +name: microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: PCO:0000001 ! population of organisms +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0001000 +name: pair of interacting organisms +def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] +is_a: BFO:0000040 +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid + +[Term] +id: PCO:0001001 +name: pair of interacting organisms of the same species +is_a: PCO:0001000 ! pair of interacting organisms + +[Term] +id: PCO:1000000 +name: migratory population +def: "A population which is participating in a migration process." [] +is_a: PCO:0000001 ! population of organisms +relationship: RO:0000056 PCO:1000001 ! population migration +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:1000001 +name: population migration +def: "A population process during which a population moves from one area to another." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Migration xsd:string + +[Term] +id: PCO:1000002 +name: human population migration +def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration +is_a: PCO:1000001 ! population migration +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000003 +name: human migratory population +def: "A migratory population of humans, travelling with the intention of settling in a new area." [] +is_a: PCO:0000027 ! collection of humans +relationship: RO:0000056 PCO:1000002 ! human population migration +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000004 +name: microbial community +def: "An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness." [] +comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. +synonym: "microbiota" BROAD [] +is_a: PCO:0000002 ! ecological community +is_a: PCO:0000044 ! multi-species collection of microbes +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string +property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string + diff --git a/src/ontology/pco-base.owl b/src/ontology/pco-base.owl new file mode 100644 index 0000000..37a491e --- /dev/null +++ b/src/ontology/pco-base.owl @@ -0,0 +1,1244 @@ + + + + + http://orcid.org/0000-0002-4366-3088 + https://orcid.org/0000-0001-8815-0078 + David Osumi-Sutherland + Jie Zheng + Pier Luigi Buttigieg + Ramona Walls + http://creativecommons.org/publicdomain/zero/1.0/ + http://purl.obolibrary.org/obo/IAO_8000001 + The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + organism or virus + Melissa Haendel + 9/18/11 + organism or virus or viroid + + + + + + + + + An individual member of a clade. + organism + mah + 7.16.2011 + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + organism + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. + + A material entity that consists of two or more organisms, viruses, or viroids. + group of organism + organism collection + May be of the same or different species. + collection of organisms + + + + + + + + + + This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed. + + A collection of organisms, all of the same species, that live in the same place. + ISBN:0878932739 + It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. + +Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. + population of organisms + + + + + + + + + + + + + + 2 + + + + + + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. + multispecies community + ISBN:0865423504 + Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. + ecological community + + + + + + + + + + + + + + + + + + + + A quality that inheres in a biological population. + See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. + quality of a population + + + + + + + + + + + + + + + + + + + + A quality that inheres in a community. + These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. + quality of an ecological community + + + + + + + + + + + + + + + + A process that has as primary participant a population. + Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + population process + + + + + + + + + + population birth rate + + + + + + + + + + population death rate + + + + + + + + + + Is a rate a quality? Population growth rate may be better classified as a process profile. + population growth rate + + + + + + + + + The maximum number of individuals that can be supported in a population that is growing according to logistic growth. + Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE. + ISBN:0878932739 + + obsolete carrying capacity + true + + + + + + + + + + The number of different species represented in an ecological community. + This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019). + adapted from http://en.wikipedia.org/wiki/Species_richness + community species richness + + + + + + + + + + A process that leads to a change in the number of individuals (positive or negative) in a population. + population growth + + + + + + + + + + A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat. + logistic population growth + + + + + + + + + + A population growth process that leads to an exponential increase in the number of individuals in a population. + exponential population growth + + + + + + + + + + predator role + + + + + + + + + + prey role + + + + + + + + + + symbiont role + + + + + + + + + + A collection of organisms that has as parts every organism of given species and no organisms of any other species. + At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. + species as a collection of organisms + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + + A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. + collection of organisms of the same species + single-species collection of organisms + + + + + + + + + + The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness. + If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity. + adapted from http://en.wikipedia.org/wiki/Species_diversity + The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. + community species diversity + + + + + + + + + + A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. + Needs axioms for family relationships. + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 + Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. + family + + + + + + + + + + A population process that ultimately leads to the death of all individuals in a population. + population extinction + + + + + + + + + + A process that ultimately leads to the death of all individuals in a population. + species extinction + + + + + + + + + If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. + + A quality of a community that reflects how close in abundance all species in a community are. + adapted from http://en.wikipedia.org/wiki/Species_evenness + community species evenness + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. + Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household + household + + + + + + + + + + This is an example population added to demonstrate the modeling pattern for collections of organisms. + red population + true + + + + + + + + + + An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. + red organism + true + + + + + + + + + + + + + + + + + + 2 + + + + + + + + A collection of organisms of the same species that has as members only humans. + human community + human population + collection of humans + + + + + + + + + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. + Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. + + These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). + community + true + + + + + + + + + + A collection of organisms that consists of two or more organisms from at least two species. + Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". + + multi-species collection of organisms + + + + + + + + + + A household in which the majority of the income of its members is derived from agricultural activities. + This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term. + agricultural household + + + + + + + + + + + + + + + + + + A material entity that is one or more organisms, viruses or viroids. + organismal entity + + + + + + + + + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. + genealogical family + Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/ + biological family + + + + + + + + + + + + + + + A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. + Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029 + GenEpiO curators + human social gathering activity + + + + + + + + + A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034 + GenEpio curators + human community event + + + + + + + + + A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030 + GenEpiO curators + party + + + + + + + + + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. + GenEpio curators + potluck + + + + + + + + + A human social gathering at which two people are married. May include a legal or social ceremony. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 + GenEpio curators + wedding + + + + + + + + + A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 + GenEpiO curators + baby shower + + + + + + + + + + + + + + + + + + 2 + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + + + + + + + 1 + + + + + + + + + pair of interacting organisms of the same species + + + + + + + + + + + + + + + + A population which is participating in a migration process. + migratory population + + + + + + + + + + A population process during which a population moves from one area to another. + https://en.wikipedia.org/wiki/Migration + The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. + population migration + + + + + + + + + + + + + + + + A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location. + https://en.wikipedia.org/wiki/Human_migration + The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration + human population migration + + + + + + + + + + + + + + + + A migratory population of humans, travelling with the intention of settling in a new area. + https://en.wikipedia.org/wiki/Human_migration + human migratory population + + + + + + + + + + + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. + A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 + http://orcid.org/0000-0002-4366-3088 + http://dx.doi.org/10.1038/ismej.2009.88 + microbiota + The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. + microbial community + + + + + + + + + A material entity that is one or more organisms, viruses or viroids. + wrong IRI form + http://purl.obolibrary.org/obo/PCO_0000031 + obsolete organismal entity + true + + + + + + + + + + + + + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community + + + + + + + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + + + + + + + microbial organism + microbe + + + + + + + + + + + + + + + + + 2 + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + diff --git a/src/ontology/pco-edit.owl b/src/ontology/pco-edit.owl index 066f3ab..621c799 100644 --- a/src/ontology/pco-edit.owl +++ b/src/ontology/pco-edit.owl @@ -14,8 +14,7 @@ , , , - , - ; + ; dc:contributor "http://orcid.org/0000-0002-4366-3088" , "https://orcid.org/0000-0001-8815-0078" ; dc:creator "David Osumi-Sutherland" , diff --git a/src/ontology/pco-full.obo b/src/ontology/pco-full.obo new file mode 100644 index 0000000..84df48c --- /dev/null +++ b/src/ontology/pco-full.obo @@ -0,0 +1,1820 @@ +format-version: 1.2 +data-version: pco/releases/2020-02-13/pco-full.owl +remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. +ontology: pco/pco-full +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string +property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: BFO:0000179 "continuant" xsd:string +property_value: BFO:0000180 "Continuant" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: BFO:0000179 "occurrent" xsd:string +property_value: BFO:0000180 "Occurrent" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "ic" xsd:string +property_value: BFO:0000180 "IndependentContinuant" xsd:string +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +is_a: BFO:0000003 ! occurrent +property_value: BFO:0000179 "process" xsd:string +property_value: BFO:0000180 "Process" xsd:string +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +is_a: BFO:0000020 ! specifically dependent continuant +property_value: BFO:0000179 "realizable" xsd:string +property_value: BFO:0000180 "RealizableEntity" xsd:string +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "sdc" xsd:string +property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +is_a: BFO:0000017 ! realizable entity +property_value: BFO:0000179 "role" xsd:string +property_value: BFO:0000180 "Role" xsd:string +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000027 +name: object aggregate +is_a: BFO:0000040 ! material entity +property_value: BFO:0000179 "object-aggregate" xsd:string +property_value: BFO:0000180 "ObjectAggregate" xsd:string +property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string +property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string +property_value: IAO:0000112 "a symphony orchestra" xsd:string +property_value: IAO:0000112 "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)" xsd:string +property_value: IAO:0000112 "defined by fiat: the aggregate of members of an organization" xsd:string +property_value: IAO:0000112 "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string +property_value: IAO:0000112 "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string +property_value: IAO:0000112 "defined via attributive delimitations such as: the patients in this hospital" xsd:string +property_value: IAO:0000112 "the aggregate of bearings in a constant velocity axle joint" xsd:string +property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:string +property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string +property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string +property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string +property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} +property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000029 +name: site +is_a: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "site" xsd:string +property_value: BFO:0000180 "Site" xsd:string +property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string +property_value: IAO:0000112 "a rabbit hole" xsd:string +property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string +property_value: IAO:0000112 "Manhattan Canyon)" xsd:string +property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string +property_value: IAO:0000112 "the Grand Canyon" xsd:string +property_value: IAO:0000112 "the hold of a ship" xsd:string +property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string +property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string +property_value: IAO:0000112 "the interior of your bedroom" xsd:string +property_value: IAO:0000112 "the interior of your office" xsd:string +property_value: IAO:0000112 "the interior of your refrigerator" xsd:string +property_value: IAO:0000112 "the lumen of your gut" xsd:string +property_value: IAO:0000112 "the Piazza San Marco" xsd:string +property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string +property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +is_a: BFO:0000002 ! continuant +property_value: BFO:0000179 "gdc" xsd:string +property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "material" xsd:string +property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant +property_value: BFO:0000179 "immaterial" xsd:string +property_value: BFO:0000180 "ImmaterialEntity" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: CARO:0001010 +name: organism or virus or viroid +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +is_a: PCO:0000031 ! organismal entity +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "organism or virus" xsd:string + +[Term] +id: CARO:0010004 +name: organism +def: "An individual member of a clade." [] +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +is_a: CARO:0001010 ! organism or virus or viroid +property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string +property_value: IAO:0000589 "organism" xsd:string + +[Term] +id: DbXref +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Definition +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: ENVO:00000070 +name: construction +def: "A feature that has been constructed by deliberate human effort." [MA:ma] +synonym: "constructed feature" EXACT [] +is_a: ENVO:01000813 ! astronomical body part +property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string + +[Term] +id: ENVO:00002297 +name: environmental feature +namespace: ENVO +def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] +comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. +is_a: BFO:0000040 ! material entity + +[Term] +id: ENVO:01000254 +name: environmental system +def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +synonym: "environment" EXACT [] +xref: EcoLexicon:environment +is_a: BFO:0000040 ! material entity +creation_date: 2013-09-23T16:04:08Z + +[Term] +id: ENVO:01000744 +name: human dwelling +def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] +is_a: ENVO:00000070 ! construction +property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string + +[Term] +id: ENVO:01000813 +name: astronomical body part +def: "A material part of an astronomical body." [] +subset: envoAstro +subset: envoPolar +is_a: ENVO:00002297 ! environmental feature + +[Term] +id: ENVO:01001369 +name: tidal mangrove shrubland +alt_id: CMECS:577 +def: "A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas." [] +comment: This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" +subset: envoCmecs +subset: envoMarine +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ENVO:01000254 ! environmental system +created_by: http://orcid.org/0000-0002-4366-3088 + +[Term] +id: GO:0007610 +name: behavior +namespace: biological_process +alt_id: GO:0044708 +def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] +comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). +subset: gocheck_do_not_manually_annotate +subset: goslim_agr +subset: goslim_flybase_ribbon +synonym: "behavioral response to stimulus" EXACT [] +synonym: "behaviour" EXACT [] +synonym: "behavioural response to stimulus" EXACT [] +synonym: "single-organism behavior" RELATED [] +xref: Wikipedia:Behavior +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-20T14:06:08Z + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0035176 +name: social behavior +namespace: biological_process +def: "Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group." [GOC:jh2, PMID:12848939, Wikipedia:Social_behavior] +comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. +synonym: "cooperative behavior" RELATED [] +synonym: "social behaviour" EXACT [] +xref: Wikipedia:Social_behavior +is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051705 ! multi-organism behavior +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0044419 +name: interspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +subset: goslim_candida +subset: goslim_pir +synonym: "interaction with another species" EXACT [] +synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051703 +name: intraspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: goslim_pir +synonym: "intraspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051704 +name: multi-organism process +namespace: biological_process +alt_id: GO:0051706 +def: "A biological process which involves another organism of the same or different species." [GOC:jl] +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "interaction between organisms" EXACT [] +synonym: "physiological interaction between organisms" EXACT [] +synonym: "physiological interaction with other organism" EXACT [] +is_a: BFO:0000015 ! process +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051705 +name: multi-organism behavior +namespace: biological_process +alt_id: GO:0023032 +alt_id: GO:0044709 +def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] +subset: goslim_pir +synonym: "behavioral interaction between organisms" EXACT [] +synonym: "behavioral interaction with other organism" EXACT [] +synonym: "behavioral signaling" NARROW [] +synonym: "behavioral signalling" NARROW [GOC:mah] +synonym: "behavioural interaction between organisms" EXACT [] +synonym: "behavioural interaction with other organism" EXACT [] +is_a: GO:0007610 ! behavior +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: IAO:0000027 +name: data item +is_a: IAO:0000030 ! information content entity + +[Term] +id: IAO:0000030 +name: information content entity +is_a: BFO:0000031 ! generically dependent continuant + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:03Z + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 +created_by: cjm +creation_date: 2018-05-20T20:55:30Z + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "source ontology module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:47Z + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:56:13Z + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies +created_by: cjm +creation_date: 2018-05-20T20:56:23Z + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract +created_by: cjm +creation_date: 2018-05-20T20:56:47Z + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide +created_by: cjm +creation_date: 2018-05-20T20:58:11Z + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:38Z + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:49Z + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "ribbon subset" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:19Z + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "antislim" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:57Z + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000118 "external import" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:00:14Z + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +created_by: cjm +creation_date: 2018-05-20T21:14:16Z + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso http://robot.obolibrary.org/reason +created_by: cjm +creation_date: 2018-05-20T21:20:33Z + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:21:12Z + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ +created_by: cjm +creation_date: 2018-05-20T21:21:21Z + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +created_by: cjm +creation_date: 2018-05-20T21:28:15Z + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-22T04:15:54Z + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: seeAlso "6.2" +created_by: cjm +creation_date: 2018-05-22T04:16:10Z + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +created_by: cjm +creation_date: 2018-05-22T04:16:28Z + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +created_by: cjm +creation_date: 2018-05-22T04:16:48Z + +[Term] +id: NCBITaxon:10239 +name: Viruses +namespace: ncbi_taxonomy +synonym: "Vira" RELATED synonym [] +synonym: "Viridae" RELATED synonym [] +synonym: "viruses" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117570 +name: Teleostomi +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:7776 ! Gnathostomata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117571 +name: Euteleostomi +namespace: ncbi_taxonomy +alt_id: NCBITaxon:40673 +synonym: "bony vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:117570 ! Teleostomi +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:12884 +name: Viroids +namespace: ncbi_taxonomy +synonym: "Viroid" RELATED synonym [] +synonym: "viroids" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131221 +name: Streptophytina +namespace: ncbi_taxonomy +synonym: "Charophyta/Embryophyta group" RELATED synonym [] +synonym: "charophyte/embryophyte group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:35493 ! Streptophyta +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131567 +name: cellular organisms +namespace: ncbi_taxonomy +synonym: "biota" RELATED synonym [] +xref: GC_ID:1 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1338369 +name: Dipnotetrapodomorpha +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:8287 ! Sarcopterygii +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437010 +name: Boreoeutheria +namespace: ncbi_taxonomy +synonym: "Boreotheria" RELATED synonym [] +xref: GC_ID:1 +xref: PMID:11743200 +xref: PMID:11791233 +is_a: NCBITaxon:9347 ! Eutheria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437180 +name: Acrogymnospermae +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2 +name: Bacteria +namespace: ncbi_taxonomy +synonym: "bacteria" RELATED blast_name [] +synonym: "eubacteria" EXACT genbank_common_name [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11542017 +xref: PMID:11542087 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:207598 +name: Homininae +namespace: ncbi_taxonomy +synonym: "Homo/Pan/Gorilla group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:9604 ! Hominidae +property_value: has_rank NCBITaxon:subfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2157 +name: Archaea +namespace: ncbi_taxonomy +synonym: "archaea" RELATED blast_name [] +synonym: "Archaebacteria" RELATED synonym [] +synonym: "Mendosicutes" RELATED synonym [] +synonym: "Metabacteria" RELATED synonym [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11541975 +xref: PMID:11542064 +xref: PMID:11542149 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:25527841 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2759 +name: Eukaryota +namespace: ncbi_taxonomy +synonym: "Eucarya" RELATED synonym [] +synonym: "Eucaryotae" RELATED synonym [] +synonym: "eucaryotes" EXACT genbank_common_name [] +synonym: "Eukarya" RELATED synonym [] +synonym: "Eukaryotae" RELATED synonym [] +synonym: "eukaryotes" EXACT common_name [] +synonym: "eukaryotes" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3041 +name: Chlorophyta +namespace: ncbi_taxonomy +synonym: "algae" RELATED in_part [] +synonym: "Chlorophycota" RELATED synonym [] +synonym: "Chlorophyta sensu Bremer 1985" RELATED synonym [] +synonym: "green algae" EXACT genbank_common_name [] +synonym: "green algae" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314146 +name: Euarchontoglires +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:11214319 +xref: PMID:12082125 +xref: PMID:12878460 +xref: PMID:15522813 +is_a: NCBITaxon:1437010 ! Boreoeutheria +property_value: has_rank NCBITaxon:superorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314293 +name: Simiiformes +namespace: ncbi_taxonomy +synonym: "Anthropoidea" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:376913 ! Haplorrhini +property_value: has_rank NCBITaxon:infraorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314295 +name: Hominoidea +namespace: ncbi_taxonomy +synonym: "ape" EXACT common_name [] +synonym: "apes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9526 ! Catarrhini +property_value: has_rank NCBITaxon:superfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3193 +name: Embryophyta +namespace: ncbi_taxonomy +synonym: "higher plants" EXACT common_name [] +synonym: "land plants" EXACT common_name [] +synonym: "land plants" RELATED blast_name [] +synonym: "plants" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:131221 ! Streptophytina +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32523 +name: Tetrapoda +namespace: ncbi_taxonomy +synonym: "tetrapods" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32524 +name: Amniota +namespace: ncbi_taxonomy +synonym: "amniotes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32523 ! Tetrapoda +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32525 +name: Theria +namespace: ncbi_taxonomy +synonym: "Theria" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:40674 ! Mammalia +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33090 +name: Viridiplantae +namespace: ncbi_taxonomy +synonym: "Chlorobionta" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] +synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "green plants" EXACT common_name [] +synonym: "green plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33154 +name: Opisthokonta +namespace: ncbi_taxonomy +synonym: "Fungi/Metazoa group" RELATED synonym [] +synonym: "opisthokonts" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33208 +name: Metazoa +namespace: ncbi_taxonomy +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33213 +name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:6072 ! Eumetazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33511 +name: Deuterostomia +namespace: ncbi_taxonomy +synonym: "deuterostomes" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33213 ! Bilateria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3398 +name: Magnoliophyta +namespace: ncbi_taxonomy +synonym: "Angiospermae" RELATED synonym [] +synonym: "angiosperms" EXACT common_name [] +synonym: "flowering plants" EXACT genbank_common_name [] +synonym: "flowering plants" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:25249442 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:35493 +name: Streptophyta +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:376913 +name: Haplorrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:9443 ! Primates +property_value: has_rank NCBITaxon:suborder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:40674 +name: Mammalia +namespace: ncbi_taxonomy +synonym: "mammals" EXACT genbank_common_name [] +synonym: "mammals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32524 ! Amniota +property_value: has_rank NCBITaxon:class +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58023 +name: Tracheophyta +namespace: ncbi_taxonomy +synonym: "vascular plants" EXACT common_name [] +synonym: "vascular plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:3193 ! Embryophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58024 +name: Spermatophyta +namespace: ncbi_taxonomy +synonym: "seed plants" EXACT common_name [] +synonym: "seed plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:78536 ! Euphyllophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33208 ! Metazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7711 +name: Chordata +namespace: ncbi_taxonomy +synonym: "chordates" EXACT genbank_common_name [] +synonym: "chordates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33511 ! Deuterostomia +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7742 +name: Vertebrata +namespace: ncbi_taxonomy +synonym: "Vertebrata" EXACT scientific_name [] +synonym: "vertebrates" EXACT genbank_common_name [] +synonym: "vertebrates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:89593 ! Craniata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7776 +name: Gnathostomata +namespace: ncbi_taxonomy +synonym: "Gnathostomata" EXACT scientific_name [] +synonym: "jawed vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7742 ! Vertebrata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:78536 +name: Euphyllophyta +namespace: ncbi_taxonomy +synonym: "euphyllophytes" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:58023 ! Tracheophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:8287 +name: Sarcopterygii +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:117571 ! Euteleostomi +property_value: has_rank NCBITaxon:superclass +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:89593 +name: Craniata +namespace: ncbi_taxonomy +synonym: "Craniata" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7711 ! Chordata +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9347 +name: Eutheria +namespace: ncbi_taxonomy +synonym: "eutherian mammals" EXACT common_name [] +synonym: "placental mammals" EXACT common_name [] +synonym: "Placentalia" RELATED synonym [] +synonym: "placentals" EXACT genbank_common_name [] +synonym: "placentals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32525 ! Theria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9443 +name: Primates +namespace: ncbi_taxonomy +synonym: "Primata" RELATED synonym [] +synonym: "primate" EXACT equivalent_name [] +synonym: "primates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:314146 ! Euarchontoglires +property_value: has_rank NCBITaxon:order +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9526 +name: Catarrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:314293 ! Simiiformes +property_value: has_rank NCBITaxon:parvorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9604 +name: Hominidae +namespace: ncbi_taxonomy +synonym: "great apes" EXACT genbank_common_name [] +synonym: "Pongidae" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:314295 ! Hominoidea +property_value: has_rank NCBITaxon:family +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9605 +name: Homo +namespace: ncbi_taxonomy +synonym: "humans" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:207598 ! Homininae +property_value: has_rank NCBITaxon:genus +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9606 +name: Homo sapiens +namespace: ncbi_taxonomy +synonym: "Home sapiens" RELATED misspelling [] +synonym: "Homo sampiens" RELATED misspelling [] +synonym: "Homo sapeins" RELATED misspelling [] +synonym: "Homo sapian" RELATED misspelling [] +synonym: "Homo sapians" RELATED misspelling [] +synonym: "Homo sapien" RELATED misspelling [] +synonym: "Homo sapience" RELATED misspelling [] +synonym: "Homo sapiense" RELATED misspelling [] +synonym: "Homo sapients" RELATED misspelling [] +synonym: "Homo sapines" RELATED misspelling [] +synonym: "Homo spaiens" RELATED misspelling [] +synonym: "Homo spiens" RELATED misspelling [] +synonym: "human" EXACT genbank_common_name [] +synonym: "Humo sapiens" RELATED misspelling [] +synonym: "man" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9605 ! Homo +property_value: has_rank NCBITaxon:species +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: PATO:0000001 +name: quality +namespace: quality +alt_id: PATO:0000072 +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +synonym: "trait" EXACT [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000161 +name: rate +namespace: quality +def: "A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time." [PATOC:melissa] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002062 ! physical quality of a process +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001236 +name: process quality +namespace: quality +alt_id: PATO:0001239 +alt_id: PATO:0001240 +def: "A quality which inheres in an process." [PATOC:GVG] +comment: See comments of relational quality of a physical entity. +synonym: "quality of a process" EXACT [] +synonym: "quality of occurrent" EXACT [] +synonym: "quality of process" EXACT [] +synonym: "relational quality of occurrent" EXACT [] +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001241 +name: physical object quality +namespace: quality +alt_id: PATO:0001237 +alt_id: PATO:0001238 +def: "A quality which inheres in a continuant." [PATOC:GVG] +comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. +synonym: "monadic quality of a continuant" EXACT [] +synonym: "monadic quality of an object" NARROW [] +synonym: "monadic quality of continuant" NARROW [] +synonym: "multiply inhering quality of a physical entity" EXACT [] +synonym: "quality of a continuant" EXACT [] +synonym: "quality of a single physical entity" EXACT [] +synonym: "quality of an object" EXACT [] +synonym: "quality of continuant" EXACT [] +xref: snap:Quality +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001338 +name: mixed sex +namespace: quality +def: "A biological sex quality inhering in a population of multiple sexes." [MGED:MGED] +comment: For example a mixture of females and male or males and hermaphrodites. +subset: value_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001415 +name: morbidity +namespace: quality +def: "A quality inhering in a population by virtue of the proportion of its members that are ill at a given time." [PATOC:GVG] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002003 +name: population quality +namespace: quality +def: "A quality that inheres in an entire population or part of a population." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002062 +name: physical quality of a process +namespace: quality +subset: attribute_slim +is_a: PATO:0001236 ! process quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +created_by: george +creation_date: 2009-06-05T09:16:46Z + +[Term] +id: PCO:0000000 +name: collection of organisms +def: "A material entity that consists of two or more organisms, viruses, or viroids." [] +comment: May be of the same or different species. +is_a: BFO:0000027 ! object aggregate +is_a: PCO:0000031 ! organismal entity +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "group of organism" xsd:string +property_value: IAO:0000118 "organism collection" xsd:string + +[Term] +id: PCO:0000001 +name: population of organisms +def: "A collection of organisms, all of the same species, that live in the same place." [] +comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000112 "" xsd:string +property_value: IAO:0000112 "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 ISBN:0878932739 xsd:string + +[Term] +id: PCO:0000002 +name: ecological community +def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] +comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +property_value: IAO:0000118 "multispecies community" xsd:string +property_value: IAO:0000119 ISBN:0865423504 xsd:string + +[Term] +id: PCO:0000003 +name: quality of a population +def: "A quality that inheres in a biological population." [] +comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. +is_a: PATO:0002003 ! population quality +intersection_of: PATO:0002003 ! population quality +intersection_of: RO:0000052 PCO:0000001 ! population of organisms +relationship: RO:0000052 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000004 +name: quality of an ecological community +def: "A quality that inheres in a community." [] +comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. +is_a: PATO:0002003 ! population quality +intersection_of: PATO:0002003 ! population quality +intersection_of: RO:0000052 PCO:0000002 ! ecological community +relationship: RO:0000052 PCO:0000002 ! ecological community +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000005 +name: population process +def: "A process that has as primary participant a population. " [] +comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +is_a: BFO:0000015 ! process +relationship: RO:0000057 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000006 +name: population birth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000007 +name: population death rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000008 +name: population growth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string + +[Term] +id: PCO:0000009 +name: obsolete carrying capacity +def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] +is_a: ObsoleteClass +property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +property_value: IAO:0000119 ISBN:0878932739 xsd:string +property_value: IAO:0000231 IAO:0000423 +is_obsolete: true + +[Term] +id: PCO:0000010 +name: community species richness +def: "The number of different species represented in an ecological community." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string + +[Term] +id: PCO:0000011 +name: population growth +def: "A process that leads to a change in the number of individuals (positive or negative) in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000012 +name: logistic population growth +def: "A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000013 +name: exponential population growth +def: "A population growth process that leads to an exponential increase in the number of individuals in a population." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000014 +name: predator role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000015 +name: prey role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000016 +name: symbiont role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000017 +name: species as a collection of organisms +def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string + +[Term] +id: PCO:0000018 +name: single-species collection of organisms +def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000118 "collection of organisms of the same species" xsd:string + +[Term] +id: PCO:0000019 +name: community species diversity +def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] +comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string + +[Term] +id: PCO:0000020 +name: family +def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] +comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string +property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string + +[Term] +id: PCO:0000021 +name: population extinction +def: "A population process that ultimately leads to the death of all individuals in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000022 +name: species extinction +def: "A process that ultimately leads to the death of all individuals in a population." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000023 +name: community species evenness +def: "A quality of a community that reflects how close in abundance all species in a community are." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_evenness" xsd:string + +[Term] +id: PCO:0000024 +name: household +def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] +is_a: PCO:0000031 ! organismal entity +relationship: RO:0002321 ENVO:01000744 ! human dwelling +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! Homo sapiens +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string + +[Term] +id: PCO:0000025 +name: red population +comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000026 +name: red organism +comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000027 +name: collection of humans +def: "A collection of organisms of the same species that has as members only humans." [] +is_a: PCO:0000018 ! single-species collection of organisms +intersection_of: PCO:0000018 ! single-species collection of organisms +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! Homo sapiens +relationship: RO:0002351 NCBITaxon:9606 ! Homo sapiens +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "human community" xsd:string +property_value: IAO:0000118 "human population" xsd:string + +[Term] +id: PCO:0000028 +name: community +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). +is_a: ObsoleteClass +property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000029 +name: multi-species collection of organisms +def: "A collection of organisms that consists of two or more organisms from at least two species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string + +[Term] +id: PCO:0000030 +name: agricultural household +name: obsolete organismal entity +def: "A household in which the majority of the income of its members is derived from agricultural activities." [] +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: ObsoleteClass +is_a: PCO:0000024 ! household +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string +property_value: IAO:0000231 "wrong IRI form" xsd:string +is_obsolete: true +replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 + +[Term] +id: PCO:0000031 +name: organismal entity +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: BFO:0000040 ! material entity +union_of: CARO:0001010 ! organism or virus or viroid +union_of: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 + +[Term] +id: PCO:0000032 +name: biological family +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +is_a: PCO:0000020 ! family +property_value: IAO:0000118 "genealogical family" xsd:string +property_value: IAO:0000119 "Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/" xsd:string + +[Term] +id: PCO:0000033 +name: human social gathering activity +def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] +is_a: GO:0035176 ! social behavior +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000034 +name: human community event +def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000035 +name: party +def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000037 +name: potluck +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string +property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000038 +name: wedding +def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000039 +name: baby shower +def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000040 +name: tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: PCO:0000002 ! ecological community +relationship: BFO:0000050 ENVO:01001369 ! tidal mangrove shrubland +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string + +[Term] +id: PCO:0000041 +name: invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: PATO:0001241 ! physical object quality + +[Term] +id: PCO:0000042 +name: microbe +synonym: "microbial organism" EXACT [] +is_a: CARO:0001010 ! organism or virus or viroid +relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye + +[Term] +id: PCO:0000043 +name: collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe +intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000044 +name: multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: PCO:0000029 ! multi-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000045 +name: single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000046 +name: microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: PCO:0000001 ! population of organisms +is_a: PCO:0000045 ! single species collection of microbes +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0001000 +name: pair of interacting organisms +def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] +is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid + +[Term] +id: PCO:0001001 +name: pair of interacting organisms of the same species +is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0001000 ! pair of interacting organisms + +[Term] +id: PCO:1000000 +name: migratory population +def: "A population which is participating in a migration process." [] +is_a: PCO:0000001 ! population of organisms +relationship: RO:0000056 PCO:1000001 ! population migration +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:1000001 +name: population migration +def: "A population process during which a population moves from one area to another." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Migration xsd:string + +[Term] +id: PCO:1000002 +name: human population migration +def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration +is_a: PCO:1000001 ! population migration +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000003 +name: human migratory population +def: "A migratory population of humans, travelling with the intention of settling in a new area." [] +is_a: PCO:0000027 ! collection of humans +relationship: RO:0000056 PCO:1000002 ! human population migration +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000004 +name: microbial community +def: "An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness." [] +comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. +synonym: "microbiota" BROAD [] +is_a: PCO:0000002 ! ecological community +is_a: PCO:0000044 ! multi-species collection of microbes +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string +property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Synonym +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: SynonymType +is_a: IAO:0000102 ! data about an ontology part + diff --git a/src/ontology/pco-full.owl b/src/ontology/pco-full.owl new file mode 100644 index 0000000..c95c12c --- /dev/null +++ b/src/ontology/pco-full.owl @@ -0,0 +1,4991 @@ + + + + + http://orcid.org/0000-0002-4366-3088 + https://orcid.org/0000-0001-8815-0078 + David Osumi-Sutherland + Jie Zheng + Pier Luigi Buttigieg + Ramona Walls + http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + editor preferred term + + + + + + + + example + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + editor note + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + alternative term + + + + + + + + definition source + + formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + + + + + is denotator type + relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from + + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + + + + + + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + + + + + + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + + has associated axiom(fol) + + + + + + + + is allocated id range + Add as annotation triples in the granting ontology + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + is allocated id range + + + + + + + + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + 2018-09-21T16:43:39Z + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + + has axiom label + + + + + + + + term replaced by + + Add as annotation triples in the granting ontology + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + term replaced by + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_alternative_id + + + + + + + + + + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + + + + + + + + + + has_obo_namespace + + + + + + + + + has_related_synonym + + + + + + + + + + + + + + + + + + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + continuant + Continuant + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + + + + + occurrent + Occurrent + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + + + + + + + + + object-aggregate + ObjectAggregate + a collection of cells in a blood biobank. + a swarm of bees is an aggregate of members who are linked together through natural bonds + a symphony orchestra + an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) + defined by fiat: the aggregate of members of an organization + defined through physical attachment: the aggregate of atoms in a lump of granite + defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container + defined via attributive delimitations such as: the patients in this hospital + the aggregate of bearings in a constant velocity axle joint + the aggregate of blood cells in your body + the nitrogen atoms in the atmosphere + the restaurants in Palo Alto + your collection of Meissen ceramic plates. + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + object aggregate + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + + + + + + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + + + + + + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + + + + + + + + + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + site + + + + + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + + + + + + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + + + + + immaterial + ImmaterialEntity + BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 + + immaterial entity + + + + + + + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + organism or virus + Melissa Haendel + 9/18/11 + organism or virus or viroid + + + + + + + + + An individual member of a clade. + organism + mah + 7.16.2011 + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + organism + + + + + + + + + A feature that has been constructed by deliberate human effort. + "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference + constructed feature + construction + + + + + A feature that has been constructed by deliberate human effort. + MA:ma + + + + + + + + + A material entity which determines an environmental system. + ENVO + ENVO:00002297 + A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. + environmental feature + + + + + A material entity which determines an environmental system. + DOI:10.1186/2041-1480-4-43 + NM:nm + ORCID:0000-0002-4366-3088 + + + + + + + + + A system which has the disposition to environ one or more material entities. + 2013-09-23T16:04:08Z + EcoLexicon:environment + environment + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + + A system which has the disposition to environ one or more material entities. + DOI:10.1186/2041-1480-4-43 + + + + + + + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. + Subclasses will be added by inference. + human dwelling + + + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 + + + + + + + + + A material part of an astronomical body. + envoAstro + envoPolar + astronomical body part + + + + + + + + + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. + http://orcid.org/0000-0002-4366-3088 + CMECS:577 + https://cmecscatalog.org/cmecs/classification/unit/577.html + envoCmecs + envoMarine + This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" + tidal mangrove shrubland + + + + + + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + janelomax + 2012-09-20T14:06:08Z + GO:0044708 + Wikipedia:Behavior + behavioral response to stimulus + behaviour + behavioural response to stimulus + biological_process + single-organism behavior + GO:0007610 + + + + 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. +2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). + + behavior + + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + GOC:ems + GOC:jl + ISBN:0395448956 + PMID:20160973 + + + + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + janelomax + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + + biological_process + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + + Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + Wikipedia:Social_behavior + social behaviour + biological_process + cooperative behavior + GO:0035176 + Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. + + social behavior + + + + + Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + GOC:jh2 + PMID:12848939 + Wikipedia:Social_behavior + + + + + + + + + Any process in which an organism has an effect on an organism of a different species. + interaction with another species + interspecies interaction + interspecies interaction with other organisms + biological_process + GO:0044419 + + + + interspecies interaction between organisms + + + + + Any process in which an organism has an effect on an organism of a different species. + GOC:cc + + + + + + + + + Any process in which an organism has an effect on an organism of the same species. + intraspecies interaction with other organisms + biological_process + GO:0051703 + + + intraspecies interaction between organisms + + + + + Any process in which an organism has an effect on an organism of the same species. + GOC:ai + + + + + + + + + + A biological process which involves another organism of the same or different species. + GO:0051706 + interaction between organisms + physiological interaction between organisms + physiological interaction with other organism + biological_process + GO:0051704 + + + + multi-organism process + + + + + A biological process which involves another organism of the same or different species. + GOC:jl + + + + + + + + + + Any process in which an organism has a behavioral effect on another organism of the same or different species. + GO:0023032 + GO:0044709 + behavioral interaction between organisms + behavioral interaction with other organism + behavioural interaction between organisms + behavioural interaction with other organism + behavioral signaling + behavioral signalling + biological_process + GO:0051705 + + + multi-organism behavior + + + + + Any process in which an organism has a behavioral effect on another organism of the same or different species. + GOC:ai + + + + + behavioral signalling + GOC:mah + + + + + + + + + data item + + + + + + + + + information content entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + cjm + 2018-05-20T20:55:03Z + ontology module + + + + + + + + + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + cjm + 2018-05-20T20:55:30Z + base ontology module + + + + + + + + + + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + cjm + 2018-05-20T20:55:47Z + editors ontology module + + + + + + + + + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + cjm + 2018-05-20T20:56:13Z + main release ontology module + + + + + + + + + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + cjm + 2018-05-20T20:56:23Z + bridge ontology module + + + + + + + + + + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + cjm + 2018-05-20T20:56:47Z + import ontology module + + + + + + + + + + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + cjm + 2018-05-20T20:58:11Z + subset ontology module + + + + + + + + + + + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + cjm + 2018-05-20T20:58:38Z + curation subset ontology module + + + + + + + + + An ontology module that is intended for usage in analysis or discovery applications. + cjm + 2018-05-20T20:58:49Z + analysis subset ontology module + + + + + + + + + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + cjm + 2018-05-20T20:59:19Z + single layer subset ontology module + + + + + + + + + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + cjm + 2018-05-20T20:59:57Z + exclusion subset ontology module + + + + + + + + + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + cjm + 2018-05-20T21:00:14Z + external import ontology module + + + + + + + + + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + cjm + 2018-05-20T21:14:16Z + species subset ontology module + + + + + + + + + + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + cjm + 2018-05-20T21:20:33Z + reasoned ontology module + + + + + + + + + + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + cjm + 2018-05-20T21:21:12Z + generated ontology module + + + + + + + + + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + cjm + 2018-05-20T21:21:21Z + template generated ontology module + + + + + + + + + + + + cjm + 2018-05-20T21:28:15Z + taxonomic bridge ontology module + + + + + + + + + cjm + 2018-05-22T04:15:54Z + ontology module subsetted by expressivity + + + + + + + + + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + cjm + 2018-05-22T04:16:10Z + obo basic subset ontology module + + + + + + + + + + cjm + 2018-05-22T04:16:28Z + ontology module subsetted by OWL profile + + + + + + + + + cjm + 2018-05-22T04:16:48Z + EL++ ontology module + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Vira + Viridae + viruses + + Viruses + + + + + Vira + + + + + + Viridae + + + + + + viruses + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Teleostomi + + + + + + + + + NCBITaxon:40673 + GC_ID:1 + bony vertebrates + ncbi_taxonomy + + Euteleostomi + + + + + bony vertebrates + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Viroid + viroids + + Viroids + + + + + Viroid + + + + + + viroids + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Charophyta/Embryophyta group + charophyte/embryophyte group + + Streptophytina + + + + + Charophyta/Embryophyta group + + + + + + charophyte/embryophyte group + + + + + + + + + GC_ID:1 + ncbi_taxonomy + biota + + cellular organisms + + + + + biota + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Dipnotetrapodomorpha + + + + + + + + + GC_ID:1 + PMID:11743200 + PMID:11791233 + ncbi_taxonomy + Boreotheria + + Boreoeutheria + + + + + Boreotheria + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Acrogymnospermae + + + + + + + + + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11542017 + PMID:11542087 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:270744 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 + eubacteria + ncbi_taxonomy + Monera + Procaryotae + Prokaryota + Prokaryotae + bacteria + prokaryote + prokaryotes + + Bacteria + + + + + prokaryotes + + + + + + eubacteria + + + + + + Monera + + + + + + Procaryotae + + + + + + Prokaryota + + + + + + Prokaryotae + + + + + + bacteria + + + + + + prokaryote + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Homo/Pan/Gorilla group + + Homininae + + + + + Homo/Pan/Gorilla group + + + + + + + + + + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11541975 + PMID:11542064 + PMID:11542149 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:25527841 + PMID:270744 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 + ncbi_taxonomy + Archaebacteria + Mendosicutes + Metabacteria + Monera + Procaryotae + Prokaryota + Prokaryotae + archaea + prokaryote + prokaryotes + + Archaea + + + + + Archaebacteria + + + + + + Mendosicutes + + + + + + Metabacteria + + + + + + Monera + + + + + + Procaryotae + + + + + + Prokaryota + + + + + + Prokaryotae + + + + + + archaea + + + + + + prokaryote + + + + + + prokaryotes + + + + + + + + + + + GC_ID:1 + PMID:23020233 + eucaryotes + eukaryotes + ncbi_taxonomy + Eucarya + Eucaryotae + Eukarya + Eukaryotae + eukaryotes + + Eukaryota + + + + + eucaryotes + + + + + + eukaryotes + + + + + + Eucarya + + + + + + Eucaryotae + + + + + + Eukarya + + + + + + Eukaryotae + + + + + + eukaryotes + + + + + + + + + + + GC_ID:1 + PMID:23020233 + green algae + ncbi_taxonomy + Chlorophycota + Chlorophyta sensu Bremer 1985 + algae + green algae + + Chlorophyta + + + + + green algae + + + + + + Chlorophycota + + + + + + Chlorophyta sensu Bremer 1985 + + + + + + algae + + + + + + green algae + + + + + + + + + + + GC_ID:1 + PMID:11214319 + PMID:12082125 + PMID:12878460 + PMID:15522813 + ncbi_taxonomy + + Euarchontoglires + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Anthropoidea + + Simiiformes + + + + + Anthropoidea + + + + + + + + + + + GC_ID:1 + ape + apes + ncbi_taxonomy + + Hominoidea + + + + + ape + + + + + + apes + + + + + + + + + + GC_ID:1 + higher plants + land plants + plants + ncbi_taxonomy + land plants + + Embryophyta + + + + + higher plants + + + + + + land plants + + + + + + plants + + + + + + land plants + + + + + + + + + + GC_ID:1 + tetrapods + ncbi_taxonomy + + Tetrapoda + + + + + tetrapods + + + + + + + + + + GC_ID:1 + amniotes + ncbi_taxonomy + + Amniota + + + + + amniotes + + + + + + + + + + GC_ID:1 + Theria + ncbi_taxonomy + + Theria <Mammalia> + + + + + Theria + + + + + + + + + + + GC_ID:1 + green plants + ncbi_taxonomy + Chlorobionta + Chlorophyta/Embryophyta group + chlorophyte/embryophyte group + green plants + + Viridiplantae + + + + + green plants + + + + + + Chlorobionta + + + + + + Chlorophyta/Embryophyta group + + + + + + chlorophyte/embryophyte group + + + + + + green plants + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + Fungi/Metazoa group + opisthokonts + + Opisthokonta + + + + + Fungi/Metazoa group + + + + + + opisthokonts + + + + + + + + + + + GC_ID:1 + metazoans + multicellular animals + ncbi_taxonomy + Animalia + animals + + Metazoa + + + + + metazoans + + + + + + multicellular animals + + + + + + Animalia + + + + + + animals + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Bilateria + + + + + + + + + GC_ID:1 + deuterostomes + ncbi_taxonomy + + Deuterostomia + + + + + deuterostomes + + + + + + + + + + GC_ID:1 + PMID:25249442 + angiosperms + flowering plants + ncbi_taxonomy + Angiospermae + flowering plants + + Magnoliophyta + + + + + angiosperms + + + + + + flowering plants + + + + + + Angiospermae + + + + + + flowering plants + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Streptophyta + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Haplorrhini + + + + + + + + + + GC_ID:1 + mammals + ncbi_taxonomy + mammals + + Mammalia + + + + + mammals + + + + + + mammals + + + + + + + + + + GC_ID:1 + vascular plants + ncbi_taxonomy + vascular plants + + Tracheophyta + + + + + vascular plants + + + + + + vascular plants + + + + + + + + + + GC_ID:1 + seed plants + ncbi_taxonomy + seed plants + + Spermatophyta + + + + + seed plants + + + + + + seed plants + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Eumetazoa + + + + + + + + + + GC_ID:1 + chordates + ncbi_taxonomy + chordates + + Chordata + + + + + chordates + + + + + + chordates + + + + + + + + + + GC_ID:1 + Vertebrata + vertebrates + ncbi_taxonomy + vertebrates + + Vertebrata <Metazoa> + + + + + Vertebrata + + + + + + vertebrates + + + + + + vertebrates + + + + + + + + + + GC_ID:1 + Gnathostomata + jawed vertebrates + ncbi_taxonomy + + Gnathostomata <vertebrate> + + + + + Gnathostomata + + + + + + jawed vertebrates + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + euphyllophytes + + Euphyllophyta + + + + + euphyllophytes + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Sarcopterygii + + + + + + + + + + GC_ID:1 + Craniata + ncbi_taxonomy + + Craniata <chordata> + + + + + Craniata + + + + + + + + + + GC_ID:1 + eutherian mammals + placental mammals + placentals + ncbi_taxonomy + Placentalia + placentals + + Eutheria + + + + + eutherian mammals + + + + + + placental mammals + + + + + + placentals + + + + + + Placentalia + + + + + + placentals + + + + + + + + + + + GC_ID:1 + primate + ncbi_taxonomy + Primata + primates + + Primates + + + + + primate + + + + + + Primata + + + + + + primates + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + + Catarrhini + + + + + + + + + + GC_ID:1 + great apes + ncbi_taxonomy + Pongidae + + Hominidae + + + + + great apes + + + + + + Pongidae + + + + + + + + + + + GC_ID:1 + humans + ncbi_taxonomy + + Homo + + + + + humans + + + + + + + + + + + GC_ID:1 + human + man + ncbi_taxonomy + Home sapiens + Homo sampiens + Homo sapeins + Homo sapian + Homo sapians + Homo sapien + Homo sapience + Homo sapiense + Homo sapients + Homo sapines + Homo spaiens + Homo spiens + Humo sapiens + + Homo sapiens + + + + + human + + + + + + man + + + + + + Home sapiens + + + + + + Homo sampiens + + + + + + Homo sapeins + + + + + + Homo sapian + + + + + + Homo sapians + + + + + + Homo sapien + + + + + + Homo sapience + + + + + + Homo sapiense + + + + + + Homo sapients + + + + + + Homo sapines + + + + + + Homo spaiens + + + + + + Homo spiens + + + + + + Humo sapiens + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATO:0000072 + trait + quality + PATO:0000001 + + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + + rate + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + PATOC:melissa + + + + + + + + + A quality which inheres in an process. + PATO:0001239 + PATO:0001240 + quality of a process + quality of occurrent + quality of process + relational quality of occurrent + quality + PATO:0001236 + See comments of relational quality of a physical entity. + + process quality + + + + + A quality which inheres in an process. + PATOC:GVG + + + + + + + + + A quality which inheres in a continuant. + PATO:0001237 + PATO:0001238 + snap:Quality + monadic quality of a continuant + multiply inhering quality of a physical entity + quality of a continuant + quality of a single physical entity + quality of an object + quality of continuant + monadic quality of an object + monadic quality of continuant + quality + PATO:0001241 + Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. + + physical object quality + + + + + A quality which inheres in a continuant. + PATOC:GVG + + + + + + + + + A biological sex quality inhering in a population of multiple sexes. + quality + PATO:0001338 + + For example a mixture of females and male or males and hermaphrodites. + + mixed sex + + + + + A biological sex quality inhering in a population of multiple sexes. + MGED:MGED + + + + + + + + + A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. + quality + PATO:0001415 + + + + morbidity + + + + + A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. + PATOC:GVG + + + + + + + + + A quality that inheres in an entire population or part of a population. + quality + PATO:0002003 + + + population quality + + + + + A quality that inheres in an entire population or part of a population. + PATOC:GVG + + + + + + + + + george + 2009-06-05T09:16:46Z + quality + PATO:0002062 + + + physical quality of a process + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. + + A material entity that consists of two or more organisms, viruses, or viroids. + group of organism + organism collection + May be of the same or different species. + collection of organisms + + + + + + + + + + This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed. + + A collection of organisms, all of the same species, that live in the same place. + ISBN:0878932739 + It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. + +Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. + population of organisms + + + + + + + + + + + + + + 2 + + + + + + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. + multispecies community + ISBN:0865423504 + Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. + ecological community + + + + + + + + + + + + + + + + + + + + + + + + + + + A quality that inheres in a biological population. + See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. + quality of a population + + + + + + + + + + + + + + + + + + + + + + + + + + + A quality that inheres in a community. + These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. + quality of an ecological community + + + + + + + + + + + + + + + + A process that has as primary participant a population. + Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + population process + + + + + + + + + + population birth rate + + + + + + + + + + population death rate + + + + + + + + + + Is a rate a quality? Population growth rate may be better classified as a process profile. + population growth rate + + + + + + + + + The maximum number of individuals that can be supported in a population that is growing according to logistic growth. + Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE. + ISBN:0878932739 + + obsolete carrying capacity + true + + + + + + + + + + The number of different species represented in an ecological community. + This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019). + adapted from http://en.wikipedia.org/wiki/Species_richness + community species richness + + + + + + + + + + A process that leads to a change in the number of individuals (positive or negative) in a population. + population growth + + + + + + + + + + A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat. + logistic population growth + + + + + + + + + + A population growth process that leads to an exponential increase in the number of individuals in a population. + exponential population growth + + + + + + + + + + predator role + + + + + + + + + + prey role + + + + + + + + + + symbiont role + + + + + + + + + + A collection of organisms that has as parts every organism of given species and no organisms of any other species. + At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. + species as a collection of organisms + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + + A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. + collection of organisms of the same species + single-species collection of organisms + + + + + + + + + + The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness. + If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity. + adapted from http://en.wikipedia.org/wiki/Species_diversity + The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. + community species diversity + + + + + + + + + + A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. + Needs axioms for family relationships. + http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 + Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. + family + + + + + + + + + + A population process that ultimately leads to the death of all individuals in a population. + population extinction + + + + + + + + + + A process that ultimately leads to the death of all individuals in a population. + species extinction + + + + + + + + + If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. + + A quality of a community that reflects how close in abundance all species in a community are. + adapted from http://en.wikipedia.org/wiki/Species_evenness + community species evenness + + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + + + + An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. + Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household + household + + + + + + + + + + This is an example population added to demonstrate the modeling pattern for collections of organisms. + red population + true + + + + + + + + + + An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. + red organism + true + + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + + A collection of organisms of the same species that has as members only humans. + human community + human population + collection of humans + + + + + + + + + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. + Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. + + These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). + community + true + + + + + + + + + + A collection of organisms that consists of two or more organisms from at least two species. + Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". + + multi-species collection of organisms + + + + + + + + + + A household in which the majority of the income of its members is derived from agricultural activities. + This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term. + agricultural household + + + + + + + + + + + + + + + + + + A material entity that is one or more organisms, viruses or viroids. + organismal entity + + + + + + + + + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. + genealogical family + Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/ + biological family + + + + + + + + + + + + + + + A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. + Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029 + GenEpiO curators + human social gathering activity + + + + + + + + + A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034 + GenEpio curators + human community event + + + + + + + + + A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030 + GenEpiO curators + party + + + + + + + + + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. + GenEpio curators + potluck + + + + + + + + + A human social gathering at which two people are married. May include a legal or social ceremony. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 + GenEpio curators + wedding + + + + + + + + + A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 + GenEpiO curators + baby shower + + + + + + + + + + + + + + + + + + 2 + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + + + + + + + 1 + + + + + + + + + + pair of interacting organisms of the same species + + + + + + + + + + + + + + + + A population which is participating in a migration process. + migratory population + + + + + + + + + + A population process during which a population moves from one area to another. + https://en.wikipedia.org/wiki/Migration + The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. + population migration + + + + + + + + + + + + + + + + A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location. + https://en.wikipedia.org/wiki/Human_migration + The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration + human population migration + + + + + + + + + + + + + + + + A migratory population of humans, travelling with the intention of settling in a new area. + https://en.wikipedia.org/wiki/Human_migration + human migratory population + + + + + + + + + + + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. + A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 + http://orcid.org/0000-0002-4366-3088 + http://dx.doi.org/10.1038/ismej.2009.88 + microbiota + The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. + microbial community + + + + + + + + + A material entity that is one or more organisms, viruses or viroids. + wrong IRI form + http://purl.obolibrary.org/obo/PCO_0000031 + obsolete organismal entity + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community + + + + + + + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + + + + + + + microbial organism + microbe + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/pco.obo b/src/ontology/pco.obo new file mode 100644 index 0000000..f15f70f --- /dev/null +++ b/src/ontology/pco.obo @@ -0,0 +1,1820 @@ +format-version: 1.2 +data-version: releases/2020-02-13 +remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. +ontology: pco +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string +property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +property_value: BFO:0000179 "continuant" xsd:string +property_value: BFO:0000180 "Continuant" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: BFO:0000179 "occurrent" xsd:string +property_value: BFO:0000180 "Occurrent" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "ic" xsd:string +property_value: BFO:0000180 "IndependentContinuant" xsd:string +property_value: IAO:0000112 "a chair" xsd:string +property_value: IAO:0000112 "a heart" xsd:string +property_value: IAO:0000112 "a leg" xsd:string +property_value: IAO:0000112 "a molecule" xsd:string +property_value: IAO:0000112 "a spatial region" xsd:string +property_value: IAO:0000112 "an atom" xsd:string +property_value: IAO:0000112 "an orchestra." xsd:string +property_value: IAO:0000112 "an organism" xsd:string +property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string +property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +is_a: BFO:0000003 ! occurrent +property_value: BFO:0000179 "process" xsd:string +property_value: BFO:0000180 "Process" xsd:string +property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string +property_value: IAO:0000112 "a process of meiosis" xsd:string +property_value: IAO:0000112 "a process of sleeping" xsd:string +property_value: IAO:0000112 "the course of a disease" xsd:string +property_value: IAO:0000112 "the flight of a bird" xsd:string +property_value: IAO:0000112 "the life of an organism" xsd:string +property_value: IAO:0000112 "your process of aging." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string +property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000017 +name: realizable entity +is_a: BFO:0000020 ! specifically dependent continuant +property_value: BFO:0000179 "realizable" xsd:string +property_value: BFO:0000180 "RealizableEntity" xsd:string +property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string +property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string +property_value: IAO:0000112 "the function of your reproductive organs" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "sdc" xsd:string +property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000023 +name: role +is_a: BFO:0000017 ! realizable entity +property_value: BFO:0000179 "role" xsd:string +property_value: BFO:0000180 "Role" xsd:string +property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string +property_value: IAO:0000112 "the priest role" xsd:string +property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string +property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string +property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string +property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string +property_value: IAO:0000112 "the student role" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string +property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000027 +name: object aggregate +is_a: BFO:0000040 ! material entity +property_value: BFO:0000179 "object-aggregate" xsd:string +property_value: BFO:0000180 "ObjectAggregate" xsd:string +property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string +property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string +property_value: IAO:0000112 "a symphony orchestra" xsd:string +property_value: IAO:0000112 "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)" xsd:string +property_value: IAO:0000112 "defined by fiat: the aggregate of members of an organization" xsd:string +property_value: IAO:0000112 "defined through physical attachment: the aggregate of atoms in a lump of granite" xsd:string +property_value: IAO:0000112 "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" xsd:string +property_value: IAO:0000112 "defined via attributive delimitations such as: the patients in this hospital" xsd:string +property_value: IAO:0000112 "the aggregate of bearings in a constant velocity axle joint" xsd:string +property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:string +property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string +property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string +property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string +property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} +property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000029 +name: site +is_a: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "site" xsd:string +property_value: BFO:0000180 "Site" xsd:string +property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string +property_value: IAO:0000112 "a rabbit hole" xsd:string +property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string +property_value: IAO:0000112 "Manhattan Canyon)" xsd:string +property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string +property_value: IAO:0000112 "the Grand Canyon" xsd:string +property_value: IAO:0000112 "the hold of a ship" xsd:string +property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string +property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string +property_value: IAO:0000112 "the interior of your bedroom" xsd:string +property_value: IAO:0000112 "the interior of your office" xsd:string +property_value: IAO:0000112 "the interior of your refrigerator" xsd:string +property_value: IAO:0000112 "the lumen of your gut" xsd:string +property_value: IAO:0000112 "the Piazza San Marco" xsd:string +property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string +property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +is_a: BFO:0000002 ! continuant +property_value: BFO:0000179 "gdc" xsd:string +property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity +property_value: BFO:0000179 "material" xsd:string +property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: IAO:0000112 "a flame" xsd:string +property_value: IAO:0000112 "a forest fire" xsd:string +property_value: IAO:0000112 "a human being" xsd:string +property_value: IAO:0000112 "a hurricane" xsd:string +property_value: IAO:0000112 "a photon" xsd:string +property_value: IAO:0000112 "a puff of smoke" xsd:string +property_value: IAO:0000112 "a sea wave" xsd:string +property_value: IAO:0000112 "a tornado" xsd:string +property_value: IAO:0000112 "an aggregate of human beings." xsd:string +property_value: IAO:0000112 "an energy wave" xsd:string +property_value: IAO:0000112 "an epidemic" xsd:string +property_value: IAO:0000112 "the undetached arm of a human being" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant +property_value: BFO:0000179 "immaterial" xsd:string +property_value: BFO:0000180 "ImmaterialEntity" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: CARO:0001010 +name: organism or virus or viroid +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +is_a: PCO:0000031 ! organismal entity +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "organism or virus" xsd:string + +[Term] +id: CARO:0010004 +name: organism +def: "An individual member of a clade." [] +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +is_a: CARO:0001010 ! organism or virus or viroid +property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string +property_value: IAO:0000589 "organism" xsd:string + +[Term] +id: DbXref +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Definition +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: ENVO:00000070 +name: construction +def: "A feature that has been constructed by deliberate human effort." [MA:ma] +synonym: "constructed feature" EXACT [] +is_a: ENVO:01000813 ! astronomical body part +property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string + +[Term] +id: ENVO:00002297 +name: environmental feature +namespace: ENVO +def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] +comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. +is_a: BFO:0000040 ! material entity + +[Term] +id: ENVO:01000254 +name: environmental system +def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +synonym: "environment" EXACT [] +xref: EcoLexicon:environment +is_a: BFO:0000040 ! material entity +creation_date: 2013-09-23T16:04:08Z + +[Term] +id: ENVO:01000744 +name: human dwelling +def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] +is_a: ENVO:00000070 ! construction +property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string + +[Term] +id: ENVO:01000813 +name: astronomical body part +def: "A material part of an astronomical body." [] +subset: envoAstro +subset: envoPolar +is_a: ENVO:00002297 ! environmental feature + +[Term] +id: ENVO:01001369 +name: tidal mangrove shrubland +alt_id: CMECS:577 +def: "A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas." [] +comment: This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" +subset: envoCmecs +subset: envoMarine +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ENVO:01000254 ! environmental system +created_by: http://orcid.org/0000-0002-4366-3088 + +[Term] +id: GO:0007610 +name: behavior +namespace: biological_process +alt_id: GO:0044708 +def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] +comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). +subset: gocheck_do_not_manually_annotate +subset: goslim_agr +subset: goslim_flybase_ribbon +synonym: "behavioral response to stimulus" EXACT [] +synonym: "behaviour" EXACT [] +synonym: "behavioural response to stimulus" EXACT [] +synonym: "single-organism behavior" RELATED [] +xref: Wikipedia:Behavior +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-20T14:06:08Z + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: janelomax +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0035176 +name: social behavior +namespace: biological_process +def: "Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group." [GOC:jh2, PMID:12848939, Wikipedia:Social_behavior] +comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. +synonym: "cooperative behavior" RELATED [] +synonym: "social behaviour" EXACT [] +xref: Wikipedia:Social_behavior +is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051705 ! multi-organism behavior +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0044419 +name: interspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +subset: goslim_candida +subset: goslim_pir +synonym: "interaction with another species" EXACT [] +synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051703 +name: intraspecies interaction between organisms +namespace: biological_process +def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: goslim_pir +synonym: "intraspecies interaction with other organisms" EXACT [] +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051704 +name: multi-organism process +namespace: biological_process +alt_id: GO:0051706 +def: "A biological process which involves another organism of the same or different species." [GOC:jl] +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "interaction between organisms" EXACT [] +synonym: "physiological interaction between organisms" EXACT [] +synonym: "physiological interaction with other organism" EXACT [] +is_a: BFO:0000015 ! process +is_a: GO:0008150 ! biological_process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0051705 +name: multi-organism behavior +namespace: biological_process +alt_id: GO:0023032 +alt_id: GO:0044709 +def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] +subset: goslim_pir +synonym: "behavioral interaction between organisms" EXACT [] +synonym: "behavioral interaction with other organism" EXACT [] +synonym: "behavioral signaling" NARROW [] +synonym: "behavioral signalling" NARROW [GOC:mah] +synonym: "behavioural interaction between organisms" EXACT [] +synonym: "behavioural interaction with other organism" EXACT [] +is_a: GO:0007610 ! behavior +is_a: GO:0051704 ! multi-organism process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: IAO:0000027 +name: data item +is_a: IAO:0000030 ! information content entity + +[Term] +id: IAO:0000030 +name: information content entity +is_a: BFO:0000031 ! generically dependent continuant + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000116 "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:03Z + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 +created_by: cjm +creation_date: 2018-05-20T20:55:30Z + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "source ontology module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:55:47Z + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:56:13Z + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies +created_by: cjm +creation_date: 2018-05-20T20:56:23Z + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract +created_by: cjm +creation_date: 2018-05-20T20:56:47Z + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide +created_by: cjm +creation_date: 2018-05-20T20:58:11Z + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:38Z + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-20T20:58:49Z + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "ribbon subset" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:19Z + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "antislim" xsd:string +created_by: cjm +creation_date: 2018-05-20T20:59:57Z + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000118 "external import" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:00:14Z + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +created_by: cjm +creation_date: 2018-05-20T21:14:16Z + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: seeAlso http://robot.obolibrary.org/reason +created_by: cjm +creation_date: 2018-05-20T21:20:33Z + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +created_by: cjm +creation_date: 2018-05-20T21:21:12Z + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ +created_by: cjm +creation_date: 2018-05-20T21:21:21Z + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +created_by: cjm +creation_date: 2018-05-20T21:28:15Z + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +created_by: cjm +creation_date: 2018-05-22T04:15:54Z + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: seeAlso "6.2" +created_by: cjm +creation_date: 2018-05-22T04:16:10Z + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +created_by: cjm +creation_date: 2018-05-22T04:16:28Z + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +created_by: cjm +creation_date: 2018-05-22T04:16:48Z + +[Term] +id: NCBITaxon:10239 +name: Viruses +namespace: ncbi_taxonomy +synonym: "Vira" RELATED synonym [] +synonym: "Viridae" RELATED synonym [] +synonym: "viruses" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117570 +name: Teleostomi +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:7776 ! Gnathostomata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:117571 +name: Euteleostomi +namespace: ncbi_taxonomy +alt_id: NCBITaxon:40673 +synonym: "bony vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:117570 ! Teleostomi +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:12884 +name: Viroids +namespace: ncbi_taxonomy +synonym: "Viroid" RELATED synonym [] +synonym: "viroids" RELATED blast_name [] +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131221 +name: Streptophytina +namespace: ncbi_taxonomy +synonym: "Charophyta/Embryophyta group" RELATED synonym [] +synonym: "charophyte/embryophyte group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:35493 ! Streptophyta +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:131567 +name: cellular organisms +namespace: ncbi_taxonomy +synonym: "biota" RELATED synonym [] +xref: GC_ID:1 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1338369 +name: Dipnotetrapodomorpha +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:8287 ! Sarcopterygii +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437010 +name: Boreoeutheria +namespace: ncbi_taxonomy +synonym: "Boreotheria" RELATED synonym [] +xref: GC_ID:1 +xref: PMID:11743200 +xref: PMID:11791233 +is_a: NCBITaxon:9347 ! Eutheria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:1437180 +name: Acrogymnospermae +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2 +name: Bacteria +namespace: ncbi_taxonomy +synonym: "bacteria" RELATED blast_name [] +synonym: "eubacteria" EXACT genbank_common_name [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11542017 +xref: PMID:11542087 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:207598 +name: Homininae +namespace: ncbi_taxonomy +synonym: "Homo/Pan/Gorilla group" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:9604 ! Hominidae +property_value: has_rank NCBITaxon:subfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2157 +name: Archaea +namespace: ncbi_taxonomy +synonym: "archaea" RELATED blast_name [] +synonym: "Archaebacteria" RELATED synonym [] +synonym: "Mendosicutes" RELATED synonym [] +synonym: "Metabacteria" RELATED synonym [] +synonym: "Monera" RELATED in_part [] +synonym: "Procaryotae" RELATED in_part [] +synonym: "Prokaryota" RELATED in_part [] +synonym: "Prokaryotae" RELATED in_part [] +synonym: "prokaryote" RELATED in_part [] +synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11541975 +xref: PMID:11542064 +xref: PMID:11542149 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:25527841 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:2759 +name: Eukaryota +namespace: ncbi_taxonomy +synonym: "Eucarya" RELATED synonym [] +synonym: "Eucaryotae" RELATED synonym [] +synonym: "eucaryotes" EXACT genbank_common_name [] +synonym: "Eukarya" RELATED synonym [] +synonym: "Eukaryotae" RELATED synonym [] +synonym: "eukaryotes" EXACT common_name [] +synonym: "eukaryotes" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3041 +name: Chlorophyta +namespace: ncbi_taxonomy +synonym: "algae" RELATED in_part [] +synonym: "Chlorophycota" RELATED synonym [] +synonym: "Chlorophyta sensu Bremer 1985" RELATED synonym [] +synonym: "green algae" EXACT genbank_common_name [] +synonym: "green algae" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314146 +name: Euarchontoglires +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:11214319 +xref: PMID:12082125 +xref: PMID:12878460 +xref: PMID:15522813 +is_a: NCBITaxon:1437010 ! Boreoeutheria +property_value: has_rank NCBITaxon:superorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314293 +name: Simiiformes +namespace: ncbi_taxonomy +synonym: "Anthropoidea" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:376913 ! Haplorrhini +property_value: has_rank NCBITaxon:infraorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:314295 +name: Hominoidea +namespace: ncbi_taxonomy +synonym: "ape" EXACT common_name [] +synonym: "apes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9526 ! Catarrhini +property_value: has_rank NCBITaxon:superfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3193 +name: Embryophyta +namespace: ncbi_taxonomy +synonym: "higher plants" EXACT common_name [] +synonym: "land plants" EXACT common_name [] +synonym: "land plants" RELATED blast_name [] +synonym: "plants" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:131221 ! Streptophytina +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32523 +name: Tetrapoda +namespace: ncbi_taxonomy +synonym: "tetrapods" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32524 +name: Amniota +namespace: ncbi_taxonomy +synonym: "amniotes" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32523 ! Tetrapoda +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:32525 +name: Theria +namespace: ncbi_taxonomy +synonym: "Theria" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:40674 ! Mammalia +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33090 +name: Viridiplantae +namespace: ncbi_taxonomy +synonym: "Chlorobionta" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] +synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "green plants" EXACT common_name [] +synonym: "green plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33154 +name: Opisthokonta +namespace: ncbi_taxonomy +synonym: "Fungi/Metazoa group" RELATED synonym [] +synonym: "opisthokonts" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:2759 ! Eukaryota +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33208 +name: Metazoa +namespace: ncbi_taxonomy +synonym: "Animalia" RELATED synonym [] +synonym: "animals" RELATED blast_name [] +synonym: "metazoans" EXACT genbank_common_name [] +synonym: "multicellular animals" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33213 +name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:6072 ! Eumetazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:33511 +name: Deuterostomia +namespace: ncbi_taxonomy +synonym: "deuterostomes" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33213 ! Bilateria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:3398 +name: Magnoliophyta +namespace: ncbi_taxonomy +synonym: "Angiospermae" RELATED synonym [] +synonym: "angiosperms" EXACT common_name [] +synonym: "flowering plants" EXACT genbank_common_name [] +synonym: "flowering plants" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:25249442 +is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:35493 +name: Streptophyta +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:376913 +name: Haplorrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:9443 ! Primates +property_value: has_rank NCBITaxon:suborder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:40674 +name: Mammalia +namespace: ncbi_taxonomy +synonym: "mammals" EXACT genbank_common_name [] +synonym: "mammals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32524 ! Amniota +property_value: has_rank NCBITaxon:class +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58023 +name: Tracheophyta +namespace: ncbi_taxonomy +synonym: "vascular plants" EXACT common_name [] +synonym: "vascular plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:3193 ! Embryophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:58024 +name: Spermatophyta +namespace: ncbi_taxonomy +synonym: "seed plants" EXACT common_name [] +synonym: "seed plants" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:78536 ! Euphyllophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:6072 +name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:33208 ! Metazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7711 +name: Chordata +namespace: ncbi_taxonomy +synonym: "chordates" EXACT genbank_common_name [] +synonym: "chordates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:33511 ! Deuterostomia +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7742 +name: Vertebrata +namespace: ncbi_taxonomy +synonym: "Vertebrata" EXACT scientific_name [] +synonym: "vertebrates" EXACT genbank_common_name [] +synonym: "vertebrates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:89593 ! Craniata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:7776 +name: Gnathostomata +namespace: ncbi_taxonomy +synonym: "Gnathostomata" EXACT scientific_name [] +synonym: "jawed vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7742 ! Vertebrata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:78536 +name: Euphyllophyta +namespace: ncbi_taxonomy +synonym: "euphyllophytes" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:58023 ! Tracheophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:8287 +name: Sarcopterygii +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:117571 ! Euteleostomi +property_value: has_rank NCBITaxon:superclass +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:89593 +name: Craniata +namespace: ncbi_taxonomy +synonym: "Craniata" EXACT scientific_name [] +xref: GC_ID:1 +is_a: NCBITaxon:7711 ! Chordata +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9347 +name: Eutheria +namespace: ncbi_taxonomy +synonym: "eutherian mammals" EXACT common_name [] +synonym: "placental mammals" EXACT common_name [] +synonym: "Placentalia" RELATED synonym [] +synonym: "placentals" EXACT genbank_common_name [] +synonym: "placentals" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:32525 ! Theria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9443 +name: Primates +namespace: ncbi_taxonomy +synonym: "Primata" RELATED synonym [] +synonym: "primate" EXACT equivalent_name [] +synonym: "primates" RELATED blast_name [] +xref: GC_ID:1 +is_a: NCBITaxon:314146 ! Euarchontoglires +property_value: has_rank NCBITaxon:order +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9526 +name: Catarrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:314293 ! Simiiformes +property_value: has_rank NCBITaxon:parvorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9604 +name: Hominidae +namespace: ncbi_taxonomy +synonym: "great apes" EXACT genbank_common_name [] +synonym: "Pongidae" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:314295 ! Hominoidea +property_value: has_rank NCBITaxon:family +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9605 +name: Homo +namespace: ncbi_taxonomy +synonym: "humans" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:207598 ! Homininae +property_value: has_rank NCBITaxon:genus +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:9606 +name: Homo sapiens +namespace: ncbi_taxonomy +synonym: "Home sapiens" RELATED misspelling [] +synonym: "Homo sampiens" RELATED misspelling [] +synonym: "Homo sapeins" RELATED misspelling [] +synonym: "Homo sapian" RELATED misspelling [] +synonym: "Homo sapians" RELATED misspelling [] +synonym: "Homo sapien" RELATED misspelling [] +synonym: "Homo sapience" RELATED misspelling [] +synonym: "Homo sapiense" RELATED misspelling [] +synonym: "Homo sapients" RELATED misspelling [] +synonym: "Homo sapines" RELATED misspelling [] +synonym: "Homo spaiens" RELATED misspelling [] +synonym: "Homo spiens" RELATED misspelling [] +synonym: "human" EXACT genbank_common_name [] +synonym: "Humo sapiens" RELATED misspelling [] +synonym: "man" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:9605 ! Homo +property_value: has_rank NCBITaxon:species +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: PATO:0000001 +name: quality +namespace: quality +alt_id: PATO:0000072 +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +synonym: "trait" EXACT [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000161 +name: rate +namespace: quality +def: "A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time." [PATOC:melissa] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002062 ! physical quality of a process +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001236 +name: process quality +namespace: quality +alt_id: PATO:0001239 +alt_id: PATO:0001240 +def: "A quality which inheres in an process." [PATOC:GVG] +comment: See comments of relational quality of a physical entity. +synonym: "quality of a process" EXACT [] +synonym: "quality of occurrent" EXACT [] +synonym: "quality of process" EXACT [] +synonym: "relational quality of occurrent" EXACT [] +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001241 +name: physical object quality +namespace: quality +alt_id: PATO:0001237 +alt_id: PATO:0001238 +def: "A quality which inheres in a continuant." [PATOC:GVG] +comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. +synonym: "monadic quality of a continuant" EXACT [] +synonym: "monadic quality of an object" NARROW [] +synonym: "monadic quality of continuant" NARROW [] +synonym: "multiply inhering quality of a physical entity" EXACT [] +synonym: "quality of a continuant" EXACT [] +synonym: "quality of a single physical entity" EXACT [] +synonym: "quality of an object" EXACT [] +synonym: "quality of continuant" EXACT [] +xref: snap:Quality +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001338 +name: mixed sex +namespace: quality +def: "A biological sex quality inhering in a population of multiple sexes." [MGED:MGED] +comment: For example a mixture of females and male or males and hermaphrodites. +subset: value_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001415 +name: morbidity +namespace: quality +def: "A quality inhering in a population by virtue of the proportion of its members that are ill at a given time." [PATOC:GVG] +subset: attribute_slim +subset: scalar_slim +is_a: PATO:0002003 ! population quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002003 +name: population quality +namespace: quality +def: "A quality that inheres in an entire population or part of a population." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0002062 +name: physical quality of a process +namespace: quality +subset: attribute_slim +is_a: PATO:0001236 ! process quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +created_by: george +creation_date: 2009-06-05T09:16:46Z + +[Term] +id: PCO:0000000 +name: collection of organisms +def: "A material entity that consists of two or more organisms, viruses, or viroids." [] +comment: May be of the same or different species. +is_a: BFO:0000027 ! object aggregate +is_a: PCO:0000031 ! organismal entity +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "group of organism" xsd:string +property_value: IAO:0000118 "organism collection" xsd:string + +[Term] +id: PCO:0000001 +name: population of organisms +def: "A collection of organisms, all of the same species, that live in the same place." [] +comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. \n\nClasses for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000112 "" xsd:string +property_value: IAO:0000112 "This a general term that can include every organism of a species living in an area or any subset of them. Subclasses can be more specific as needed." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 ISBN:0878932739 xsd:string + +[Term] +id: PCO:0000002 +name: ecological community +def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] +comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +property_value: IAO:0000118 "multispecies community" xsd:string +property_value: IAO:0000119 ISBN:0865423504 xsd:string + +[Term] +id: PCO:0000003 +name: quality of a population +def: "A quality that inheres in a biological population." [] +comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. +is_a: PATO:0002003 ! population quality +intersection_of: PATO:0002003 ! population quality +intersection_of: RO:0000052 PCO:0000001 ! population of organisms +relationship: RO:0000052 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000004 +name: quality of an ecological community +def: "A quality that inheres in a community." [] +comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. +is_a: PATO:0002003 ! population quality +intersection_of: PATO:0002003 ! population quality +intersection_of: RO:0000052 PCO:0000002 ! ecological community +relationship: RO:0000052 PCO:0000002 ! ecological community +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string + +[Term] +id: PCO:0000005 +name: population process +def: "A process that has as primary participant a population. " [] +comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +is_a: BFO:0000015 ! process +relationship: RO:0000057 PCO:0000001 ! population of organisms +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000006 +name: population birth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000007 +name: population death rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000008 +name: population growth rate +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string + +[Term] +id: PCO:0000009 +name: obsolete carrying capacity +def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] +is_a: ObsoleteClass +property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +property_value: IAO:0000119 ISBN:0878932739 xsd:string +property_value: IAO:0000231 IAO:0000423 +is_obsolete: true + +[Term] +id: PCO:0000010 +name: community species richness +def: "The number of different species represented in an ecological community." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string + +[Term] +id: PCO:0000011 +name: population growth +def: "A process that leads to a change in the number of individuals (positive or negative) in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000012 +name: logistic population growth +def: "A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000013 +name: exponential population growth +def: "A population growth process that leads to an exponential increase in the number of individuals in a population." [] +is_a: PCO:0000011 ! population growth +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000014 +name: predator role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000015 +name: prey role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000016 +name: symbiont role +is_a: BFO:0000023 ! role +property_value: IAO:0000114 IAO:0000124 + +[Term] +id: PCO:0000017 +name: species as a collection of organisms +def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string + +[Term] +id: PCO:0000018 +name: single-species collection of organisms +def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000118 "collection of organisms of the same species" xsd:string + +[Term] +id: PCO:0000019 +name: community species diversity +def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] +comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string + +[Term] +id: PCO:0000020 +name: family +def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] +comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. +is_a: PCO:0000018 ! single-species collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string +property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string + +[Term] +id: PCO:0000021 +name: population extinction +def: "A population process that ultimately leads to the death of all individuals in a population." [] +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000022 +name: species extinction +def: "A process that ultimately leads to the death of all individuals in a population." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:0000023 +name: community species evenness +def: "A quality of a community that reflects how close in abundance all species in a community are." [] +is_a: PCO:0000004 ! quality of an ecological community +property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_evenness" xsd:string + +[Term] +id: PCO:0000024 +name: household +def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] +is_a: PCO:0000031 ! organismal entity +relationship: RO:0002321 ENVO:01000744 ! human dwelling +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! Homo sapiens +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string + +[Term] +id: PCO:0000025 +name: red population +comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000026 +name: red organism +comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000002 +is_obsolete: true + +[Term] +id: PCO:0000027 +name: collection of humans +def: "A collection of organisms of the same species that has as members only humans." [] +is_a: PCO:0000018 ! single-species collection of organisms +intersection_of: PCO:0000018 ! single-species collection of organisms +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! Homo sapiens +relationship: RO:0002351 NCBITaxon:9606 ! Homo sapiens +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "human community" xsd:string +property_value: IAO:0000118 "human population" xsd:string + +[Term] +id: PCO:0000028 +name: community +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). +is_a: ObsoleteClass +property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000029 +name: multi-species collection of organisms +def: "A collection of organisms that consists of two or more organisms from at least two species." [] +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string + +[Term] +id: PCO:0000030 +name: agricultural household +name: obsolete organismal entity +def: "A household in which the majority of the income of its members is derived from agricultural activities." [] +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: ObsoleteClass +is_a: PCO:0000024 ! household +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string +property_value: IAO:0000231 "wrong IRI form" xsd:string +is_obsolete: true +replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 + +[Term] +id: PCO:0000031 +name: organismal entity +def: "A material entity that is one or more organisms, viruses or viroids." [] +is_a: BFO:0000040 ! material entity +union_of: CARO:0001010 ! organism or virus or viroid +union_of: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000120 + +[Term] +id: PCO:0000032 +name: biological family +def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] +is_a: PCO:0000020 ! family +property_value: IAO:0000118 "genealogical family" xsd:string +property_value: IAO:0000119 "Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/" xsd:string + +[Term] +id: PCO:0000033 +name: human social gathering activity +def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] +is_a: GO:0035176 ! social behavior +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000034 +name: human community event +def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000035 +name: party +def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000037 +name: potluck +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string +property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000038 +name: wedding +def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: IAO:0000119 "GenEpio curators" xsd:string + +[Term] +id: PCO:0000039 +name: baby shower +def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] +is_a: PCO:0000033 ! human social gathering activity +property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: IAO:0000119 "GenEpiO curators" xsd:string + +[Term] +id: PCO:0000040 +name: tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: PCO:0000002 ! ecological community +relationship: BFO:0000050 ENVO:01001369 ! tidal mangrove shrubland +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string + +[Term] +id: PCO:0000041 +name: invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: PATO:0001241 ! physical object quality + +[Term] +id: PCO:0000042 +name: microbe +synonym: "microbial organism" EXACT [] +is_a: CARO:0001010 ! organism or virus or viroid +relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye + +[Term] +id: PCO:0000043 +name: collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe +intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000044 +name: multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: PCO:0000029 ! multi-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000045 +name: single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000043 ! collection of microbial organisms +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0000046 +name: microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: PCO:0000001 ! population of organisms +is_a: PCO:0000045 ! single species collection of microbes +relationship: RO:0002351 PCO:0000042 ! microbe +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string + +[Term] +id: PCO:0001000 +name: pair of interacting organisms +def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] +is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid + +[Term] +id: PCO:0001001 +name: pair of interacting organisms of the same species +is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0001000 ! pair of interacting organisms + +[Term] +id: PCO:1000000 +name: migratory population +def: "A population which is participating in a migration process." [] +is_a: PCO:0000001 ! population of organisms +relationship: RO:0000056 PCO:1000001 ! population migration +property_value: IAO:0000114 IAO:0000123 + +[Term] +id: PCO:1000001 +name: population migration +def: "A population process during which a population moves from one area to another." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. +is_a: PCO:0000005 ! population process +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Migration xsd:string + +[Term] +id: PCO:1000002 +name: human population migration +def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] +comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration +is_a: PCO:1000001 ! population migration +relationship: RO:0000057 PCO:0000027 ! collection of humans +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000003 +name: human migratory population +def: "A migratory population of humans, travelling with the intention of settling in a new area." [] +is_a: PCO:0000027 ! collection of humans +relationship: RO:0000056 PCO:1000002 ! human population migration +property_value: IAO:0000114 IAO:0000123 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string + +[Term] +id: PCO:1000004 +name: microbial community +def: "An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness." [] +comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. +synonym: "microbiota" BROAD [] +is_a: PCO:0000002 ! ecological community +is_a: PCO:0000044 ! multi-species collection of microbes +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string +property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: Synonym +is_a: IAO:0000102 ! data about an ontology part + +[Term] +id: SynonymType +is_a: IAO:0000102 ! data about an ontology part + diff --git a/src/ontology/pco.owl b/src/ontology/pco.owl index 26ca49d..4ce4e18 100644 --- a/src/ontology/pco.owl +++ b/src/ontology/pco.owl @@ -1,37 +1,27 @@ + xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - - - - - - - - The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. + http://orcid.org/0000-0002-4366-3088 - Ramona Walls + https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg + Ramona Walls http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. @@ -53,6 +43,22 @@ + + + + + + + + + + + + + + + + @@ -71,9 +77,10 @@ example - A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage @@ -132,6 +139,7 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition @@ -146,6 +154,8 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + + editor note editor note @@ -157,7 +167,7 @@ We also have the outstanding issue of how to aim different definitions to differ term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor @@ -187,6 +197,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source @@ -216,6 +227,34 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + @@ -276,10 +315,8 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. first order logic expression - An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. PERSON:Alan Ruttenberg first order logic expression - @@ -382,6 +419,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + elucidation @@ -394,6 +432,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language + has associated axiom(nl) @@ -406,6 +445,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax + has associated axiom(fol) @@ -423,6 +463,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + 2018-09-21T16:43:39Z + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + @@ -430,6 +498,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + has axiom label @@ -461,11061 +530,1169 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + - - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation - https://github.com/oborel/obo-relations/wiki/ROAndTime - + + - + - - tooth SubClassOf 'never in taxon' value 'Aves' - x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - Chris Mungall - - - ?X DisjointWith RO_0002162 some ?Y - never in taxon - - - + - + - - A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. - non-overlapping with - shares no parts with - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) - mutually spatially disjoint with - - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - + - + - - An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. - taxonomic class assertion - - - + - + - - S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] - ambiguous for taxon - - - + - + - - S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - https://orcid.org/0000-0002-6601-2165 - - This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost - dubious for taxon - - - + - + - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - https://orcid.org/0000-0002-6601-2165 - - present in taxon - - - + - + - - defined by inverse - - + - + - - An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. - logical macro assertion - https://github.com/oborel/obo-relations/wiki/ShortcutRelations - + - + - - An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. - annotation property cardinality - - - + - + - - A logical macro assertion whose domain is an IRI for a class - The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL - logical macro assertion on a class - - + - + - - A logical macro assertion whose domain is an IRI for a property - logical macro assertion on a property - - + - + - - logical macro assertion on an object property - - + - + - - logical macro assertion on an annotation property - - + - + - - An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. - dispositional interpretation - - + - + - - 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' - A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. - shares no connection with - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) - has no connections with - - + - + - - inherited annotation property - + - + - - Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) - curator guidance link - - + - + - - brain always_present_in_taxon 'Vertebrata' - forelimb always_present_in_taxon Euarchontoglires - S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S - This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. - never lost in - always present in taxon - + + - + - - This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. - temporal logical macro assertion on a class - + + - + - - measurement property has unit - + + + has_alternative_id - + - - has start time value - - + - + - - has end time value - + + - + - - Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. - start, days post fertilization - + + + has_exact_synonym - + - - Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. - end, days post fertilization - + + - + - - Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. - start, years post birth - + + + has_obo_namespace - + - - Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 - end, years post birth - + + + has_related_synonym - + - - Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. - start, months post birth - + + - + - - Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 - end, months post birth - + + - + - - Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. - month of gestation - + + + in_subset - + - - A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process - has developmental stage marker - + + - + - - Count of number of days intervening between the start of the stage and the time of coitum. - For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) - start, days post coitum - - + + + - + - - Count of number of days intervening between the end of the stage and the time of coitum. - end, days post coitum - + + - + - - start, weeks post birth - - + + + - + - - end, weeks post birth - - - + - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p - is asymmetric relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - + + + - + - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p - is symmetric relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - + + + - + - - R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process - is relational form of process class - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - + - - relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y - The general property hierarchy is: + + - "directly P" SubPropertyOf "P" - Transitive(P) -Where we have an annotation assertion + - "directly P" "is direct form of" "P" - If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - Chris Mungall - is direct form of - - + - + - - relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y - Chris Mungall - is indirect form of - - + - + - - logical macro assertion on an axiom - - + - + - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - + - + - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - + - + - - An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. - is relational form of a class - - + - + - - A shortcut relationship that holds between two entities based on their identity criteria - logical macro assertion involving identity - - + - + - - A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. - in approximate one to one relationship with - - + - + - - x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y - The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" - is approximately equivalent to - - + - + - - 'anterior end of organism' is-opposite-of 'posterior end of organism' - 'increase in temperature' is-opposite-of 'decrease in temperature' - x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - is opposite of - - - + - - x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - is indistinguishable from - - + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + - + - - evidential logical macro assertion on an axiom - - + + + + continuant + Continuant + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + - + - - A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. - axiom has evidence - - + + + occurrent + Occurrent + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + - + - - A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. - axiom contradicted by evidence - - + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + - - - - In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. - this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. - If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion - is representative IRI for equivalence set - OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member - - - - - - - - - eco subset - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - subset_property - - - - - - - - - - - - - - - - - - - - has_broad_synonym - - - - - - - - database_cross_reference - - - - - - - - has_exact_synonym - - - - - - - - - - - - - - has_obo_format_version - - - - - - - - has_related_synonym - - - - - - - - - - - - - - - - - - - - in_subset - - - - - - - - shorthand - - - - - - - - - - - - - - is defined by - - - - - is defined by - This is an experimental annotation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - - - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - accidentally included in BFO 1.2 proposal - - should have been BFO_0000062 - obsolete preceded by - - - - - - - - - - - - - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - precedes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - sardine has consumer some homo sapiens - - 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. - Damion Dooley - has consumer - - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - bearer of - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - inverse of has disposition - - disposition of - - - - - - - - - - A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. - David Osumi-Sutherland - (forall (?x ?y) - (iff - (neural_circuit_path ?x ?y) - (and - ("neuron ; CL_0000540" ?x) - ("neuron ; CL_0000540" ?y) - (or - (synapsed_by ?x ?y) - (synapsed_to ?x ?y))))) - -(forall (...s ?x ?y ?z) - (iff - (neural_circuit_path ...s ?x ?y ?z) - (and - (neural_circuit_path ...s ?x ?y) - ("neuron ; CL_0000540" ?z) - (or - (synapsed_by ?y ?z) - (synapsed_to ?y ?z))))) - -(forall (?x ?y) - (iff - (in_neural_circuit_with ?x ?y) - (exists (...s) - (neural_circuit_path ?x ...s ?y)))) - - - in neural circuit with - - - - - - - - - - - A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. - David Osumi-Sutherland - (forall (?x ?y) - (iff - (upstream_neural_circuit_path ?x ?y) - (and - ("neuron ; CL_0000540" ?x) - ("neuron ; CL_0000540" ?y) - (synapsed_to ?x ?y)))) - - -(forall (...s ?x ?y ?z) - (iff - (upstream_neural_circuit_path ...s ?x ?y ?z ) - (and - (upstream_neural_circuit_path ...s ?x ?y) - ("neuron ; CL_0000540" ?z) - (synapsed_to ?y ?z)))) - -(forall (?x ?y) - (iff - (upstream_in_neural_circuit_with ?x ?y) - (exists (...s) - (upstream_neural_circuit_path ?x ...s ?y)))) - - - upstream in neural circuit with - - - - - - - - - - - A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. - David Osumi-Sutherland - (forall (?x ?y) - (iff - (downstream_neural_circuit_path ?x ?y) - (and - ("neuron ; CL_0000540" ?x) - ("neuron ; CL_0000540" ?y) - (synapsed_by ?x ?y)))) - - -(forall (...s ?x ?y ?z) - (iff - (downstream_neural_circuit_path ...s ?x ?y ?z ) - (and - (downstream_neural_circuit_path ...s ?x ?y) - ("neuron ; CL_0000540" ?z) - (synapsed_by ?y ?z)))) - -(forall (?x ?y) - (iff - (downstream_in_neural_circuit_with ?x ?y) - (exists (...s) - (downstream_neural_circuit_path ?x ...s ?y)))) - - - - downstream in neural circuit with - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. - - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - location_of - - location of - - - - - - - - - - - - - - - contained in - Containment is location not involving parthood, and arises only where some immaterial continuant is involved. - Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - - contained_in - - - contained in - - - - - - - - contains - - - contains - - - - - - - - - - - penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - is allergic trigger for - - - - - - - - - - - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - is autoimmune trigger for - - - - - - - - - - penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - has allergic trigger - - - - - - - - - - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - has autoimmune trigger - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - located in - - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - David Osumi-Sutherland - - aligned with - - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - David Osumi-Sutherland - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - A relation that holds between two neurons that are electrically coupled via gap junctions. - David Osumi-Sutherland - - electrically_synapsed_to - - - - - - - - - The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - David Osumi-Sutherland - tracheates - - - - - - - - - David Osumi-Sutherland - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - innervated_by - - - - - - - - - - David Osumi-Sutherland - has synaptic terminal of - - - - - - - - - - - - - - - - - - - - - X outer_layer_of Y iff: -. X :continuant that bearer_of some PATO:laminar -. X part_of Y -. exists Z :surface -. X has_boundary Z -. Z boundary_of Y - -has_boundary: http://purl.obolibrary.org/obo/RO_0002002 -boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - - A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. - bounding layer of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. - Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland - - Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. - coincident with - - - - - - - - - - A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. - David Osumi-Sutherland - x 'cell expresses' y iff: -cell(x) -AND gene(y) -AND exists some 'transcription, DNA templated (GO_0006351)'(t) -AND t occurs_in x -AND t has_input y - cell expresses - - - - - - - - - - - x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - David Osumi-Sutherland - regulates in other organism - - - - - - - - - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - David Osumi-Sutherland - - regulates transport of - - - - - - - - - - - - A part of relation that applies only between occurents. - occurent part of - - - - - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - has positive regulatory component activity - - - - - - - - - - dos - 2017-05-24T09:36:08Z - A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. - has necessary component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - has component activity - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - has component process - - - - - - - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos - 2017-07-19T17:30:36Z - has ligand - - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - GOC:dos - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - David Osumi-Sutherland - <= - - Primitive instance level timing relation between events - before or simultaneous with - - - - - - - - - - David Osumi-Sutherland - - t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with - - - - - - - - - - David Osumi-Sutherland - - t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) - before - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which ends - - - - - - - - - - - David Osumi-Sutherland - di - Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - encompasses - - - - - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - ends after - - - - - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - immediately preceded by - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which starts - - - - - - - - - - - - - - David Osumi-Sutherland - - starts before - - - - - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - immediately precedes - - - - - - - - - - - David Osumi-Sutherland - io - - X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) - starts during - - - - - - - - - - David Osumi-Sutherland - d - during - - X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) - happens during - - - - - - - - - David Osumi-Sutherland - o - overlaps - - X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). - ends during - - - - - - - - - - - - - - - Relation between a neuron and an anatomical structure that its soma is part of. - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - - has soma location - - - - - - - - - - - - - - - - - - - - - - - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - David Osumi-Sutherland - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - fasciculates with - - - - - - - - - - - - - - - - Relation between a neuron and some structure its axon forms (chemical) synapses in. - Chris Mungall - David Osumi-Sutherland - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( - <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - - axon synapses in - - - - - - - - - - - - - - - - - - - - - - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - Chris Mungall - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - synapsed by - - - - - - - - - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - Alexander Diehl - Chris Mungall - Lindsay Cowell - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - - has plasma membrane part - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_Ib_bouton_to - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_Is_bouton_to - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_II_bouton_to - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_II_bouton - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_Ib_bouton - - - - - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - Chris Mungall - David Osumi-Sutherland - synapsed in - http://purl.obolibrary.org/obo/BFO_0000051 some ( - http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( - http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - - has postsynaptic terminal in - - - - - - - - - - has neurotransmitter - releases neurotransmitter - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - David Osumi-Sutherland - Marta Costa - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_Is_bouton - - - - - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - - has presynaptic terminal in - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type III bouton. - BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_III_bouton_to - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type III bouton. - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_III_bouton - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - Chris Mungall - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - N1 synapsed_to some N2 -Expands to: -N1 SubclassOf ( - has_part some ( - ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( - ‘synapse ; GO:0045202’ that has_part some ( - ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) - synapsed to - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - - - Chris Mungall - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( - http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( - <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - - dendrite synapsed in - - - - - - - - - - - - - - - - - - - - - - - - - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - David Osumi-Sutherland - has synapse in - <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - - has synaptic terminal in - - - - - - - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - - - overlaps - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - David Osumi-Sutherland - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - - has fasciculating neuron projection - - - - - - - - - - - - - - - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. -T innervates some R -Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - David Osumi-Sutherland - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - innervates - - - - - - - - - - - - X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - continuous with - FMA:85972 - - - - - - - - - - x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x - We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) - (iff - (proper_overlaps ?x ?y) - (and - (overlaps ?x ?y) - (not (part_of ?x ?y)) - (not (part_of ?y ?x))))) - - - partially overlaps - - - - - - - - - - - - d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. - ancestral_stucture_of - evolutionarily_descended_from - derived by descent from - - - - - - - - - - - inverse of derived by descent from - - has derived by descendant - - - - - - - - - - - - - - - - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - VBO calls this homologous_to - shares ancestor with - - - - - - - - - - - - serially homologous to - - - - - - - - - lactation SubClassOf 'only in taxon' some 'Mammalia' - - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. - The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. - - 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - Chris Mungall - - - only in taxon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - Chris Mungall - Jennifer Deegan - - - - Connects a biological entity to its taxon of origin. - in taxon - - - - - - - - - - - A is spatially_disjoint_from B if and only if they have no parts in common - There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy - BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - - - spatially disjoint from - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - - - - - - - - - - - - - - - - - - - - - - - - - - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - connected to - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - - - - - - - - - - - - - - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - connects - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - - - - - - - - - - - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of - - - - - - - - - true - - - - - - - - - Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - supplies - - - - - - - - - Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - drains - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - has component - - - - - - - - - - - - - A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - Chris Mungall - - has phenotype - - - - - - - - - - - inverse of has phenotype - Chris Mungall - - - phenotype of - - - - - - - - - - - - - - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan - This is the transitive form of the develops from relation - develops from - - - - - - - - - - - - - inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan - - develops into - - - - - - - - - - - - - - - - - definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" - We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. - Chris Mungall - gene product of - - - - - - - - - - - - - - - every HOTAIR lncRNA is the gene product of some HOXC gene - every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene - - x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y - Chris Mungall - has gene product - - - - - - - - - - - - - - - - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - Chris Mungall - expressed in - - - - - - - - - - - - - - - - - - - - - - - - - - - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y - Chris Mungall - David Osumi-Sutherland - has developmental precursor - FBbt - - TODO - add child relations from DOS - directly develops from - - - - - - - - - - A parasite that kills or sterilizes its host - parasitoid of - - - - - - - - - inverse of parasitoid of - - has parasitoid - - - - - - - - - - inverse of directly develops from - developmental precursor of - - directly develops into - - - - - - - - - - - - - - - - - - - - - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit - Chris Mungall - David Hill - Tanya Berardini - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - regulates - - - - - - - - - - - - - - - - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. - Chris Mungall - - negatively regulates (process to process) - negatively regulates - - - - - - - - - - - - - - - - - - - - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. - Chris Mungall - - positively regulates (process to process) - positively regulates - - - - - - - - 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) - heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') - - x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. - Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) - This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - Chris Mungall - has prototype - - - - - - - - - - - - - - - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' - - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) - - capable of - - - - - - - - - - - - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall - has function in - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) - capable of part of - - - - - - - - - true - - - - - - - - - - - x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall - agent in - actively participates in - - - - - - - - - 'heart development' has active participant some Shh protein - - x has participant y if and only if x realizes some active role that inheres in y - This may be obsoleted and replaced by the original 'has agent' relation - Chris Mungall - has agent - - has active participant - - - - - - - - - - - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall - - surrounded by - - - - - - - - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - - x adjacent to y if and only if x and y share a boundary. - This relation acts as a join point with BSPO - Chris Mungall - - adjacent to - - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - - - - - - - - - - inverse of surrounded by - Chris Mungall - - - surrounds - - - - - - - - - - - Chris Mungall - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporally related to - - - - - - - - - - - - inverse of starts with - Chris Mungall - Allen - - starts - - - - - - - - - - - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall - started by - - starts with - - - - - - - - - - - - - - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall - develops from part of - - - - - - - - - - - - - - - x develops_in y if x is located in y whilst x is developing - Chris Mungall - EHDAA2 - Jonathan Bard, EHDAA2 - develops in - - - - - - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - obligate parasite of - - - - - - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - facultative parasite of - - - - - - - - - - - - inverse of ends with - Chris Mungall - - ends - - - - - - - - - - - - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall - finished by - - ends with - - - - - - - - - - - - - - - - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall - starts with process that occurs in - - has start location - - - - - - - - - - - - - - - - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall - ends with process that occurs in - - has end location - - - - - - - - - - - - - - - - - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall - consumes - - has input - - - - - - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. - Chris Mungall - produces - - has output - - - - - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - stem parasite of - - - - - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - root parasite of - - - - - - - - - A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. - hemiparasite of - - - - - - - - - A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. - ExO:0000001 - has exposure receptor - - - - - - - - - A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. - ExO:0000000 - has exposure stressor - - - - - - - - - A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor - ExO:0000055 - has exposure route - - - - - - - - - A broad relationship between an exposure event or process and the course takes from the source to the target. - http://purl.obolibrary.org/obo/ExO_0000004 - has exposure transport path - - - - - - - - - - Any relationship between an exposure event or process and any other entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. - related via exposure to - - - - - - - - - g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. - over-expressed in - - - - - - - - - g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. - under-expressed in - - - - - - - - - - Any portion of roundup 'has active ingredient' some glyphosate - A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. - has active substance - has active pharmaceutical ingredient - has active ingredient - - - - - - - - - inverse of has active ingredient - - active ingredient in' - - - - - - - - - - b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - connecting branch of - - - - - - - - - inverse of connecting branch of - - has connecting branch - - - - - - - - - - - - - - - - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - - x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall - has developmental contribution from - - - - - - - - - - - - - - - inverse of has developmental contribution from - Chris Mungall - - developmentally contributes to - - - - - - - - - - - - - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - developmentally induced by - - - - - - - - - - - Inverse of developmentally induced by - Chris Mungall - developmentally induces - - - - - - - - - - - - - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p - false - Chris Mungall - In general you should not use this relation to make assertions - use one of the more specific relations below this one - This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by - - - - - - - - - c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) - has biological role - - - - - - - - - c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) - has application role - - - - - - - - - c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) - has chemical role - - - - - - - - - - - - - c involved in regulation of p if c enables 'p' and p' causally upstream of p - acts upstream of - - - - - - - - - - - - - c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p - affects - acts upstream of or within - - - - - - - - - - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else - This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - Chris Mungall - replaces - developmentally replaces - - - - - - - - - - Inverse of developmentally preceded by - Chris Mungall - developmentally succeeded by - - - - - - - - - - - - - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - Chris Mungall - part of developmental precursor of - - - - - - - - - - - x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x - Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. - Chris Mungall - ubiquitously expressed in - - - - - - - - - - Inverse of 'expressed in' - Chris Mungall - expresses - - - - - - - - - - inverse of ubiquiotously expressed in - Chris Mungall - - ubiquitously expresses - - - - - - - - - - - - p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). - This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall - results_in_developmental_progression_of - results in developmental progression of - - - - - - - - - - - every flower development (GO:0009908) results in development of some flower (PO:0009046) - - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml - results_in_development_of - results in development of - - - - - - - - - - - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_formation_of - results in formation of - - - - - - - - - - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_morphogenesis_of - results in morphogenesis of - - - - - - - - - - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_maturation_of - results in maturation of - - - - - - - - - foramen ovale closure SubClassOf results in disappearance of foramen ovale - - Chris Mungall - May be merged into parent relation - results_in_disappearance_of - results in disappearance of - - - - - - - - - every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - - Chris Mungall - May be merged into parent relation - results in developmental regression of - - - - - - - - - - Inverse of 'is substance that treats' - cjm - - is treated by substance - - - - - - - - - - - Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' -where -'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview - - x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg - adapted for living in - - A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. - has habitat - - - - - - - - - cjm - holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y - causally upstream of, positive effect - - - - - - - - - cjm - holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y - causally upstream of, negative effect - - - - - - - - - A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - Austin Meier - Chris Mungall - Marie Angelique Laporte - cjm - 2017-06-05T17:35:04Z - has exposure stimulus - - - - - - - - - Chris Mungall - evolutionary variant of - - - - - - - - - - - - - - Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c - Chris Mungall - regulates location of - transports - transports or maintains localization of - - - - - - - - - - - - - - - - - q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. - Because part_of is transitive, inheres in is a sub-relation of inheres in part of - Chris Mungall - - - inheres in part of - - - - - - - - - true - - - - - - - - - - - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. - The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_acquisition_of_features_of - results in acquisition of features of - - - - - - - - A relationship that holds via some environmental process - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. - evolutionarily related to - - - - - - - - A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions - - ecologically related to - - - - - - - - - An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - Chris Mungall - adapted for - - confers advantage in - - - - - - - - A mereological relationship or a topological relationship - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - - mereotopologically related to - - - - - - - - A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development - developmentally related to - - - - - - - - - - - Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) - a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - Chris Mungall - http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with - In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - Gene Ontology Consortium - colocalizes with - - - - - - - - - - ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. - Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. - eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex - We would like to say - -if and only if - exists c', p' - c part_of c' and c' capable_of p - and - c capable_of p' and p' part_of p -then - c contributes_to p - -However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall - http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to - In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. - contributes to - - - - - - - - - - - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity - Chris Mungall - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. - enables - - - - - - - - Chris Mungall - This is a grouping relation that collects relations used for the purpose of connecting structure and function - functionally related to - - - - - - - - - - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall - false - part of structure that is capable of - - - - - - - - - true - - - - - - - - - - holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism - genomically related to - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall - actively involved in - enables part of - involved in - - - - - - - - - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid - p regulates levels of c if p regulates some amount (PATO:0000070) of c - Chris Mungall - - regulates levels of (process to entity) - regulates levels of - - - - - - - - - - - - - - inverse of enables - Chris Mungall - enabled by - - - - - - - - - - - - inverse of regulates - Chris Mungall - regulated by (processual) - - regulated by - - - - - - - - - inverse of negatively regulates - Chris Mungall - - negatively regulated by - - - - - - - - - inverse of positively regulates - Chris Mungall - - positively regulated by - - - - - - - - - - A relationship that holds via some process of localization - Chris Mungall - related via localization to - - - - - - - - - - - - - This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - Chris Mungall - has target start location - - - - - - - - - - - - - This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - Chris Mungall - has target end location - - - - - - - - - - - - - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - Chris Mungall - imports - - - - - - - - - Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - Chris Mungall - results in transport along - - - - - - - - - Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - Chris Mungall - results in transport across - - - - - - - - - - 'pollen tube growth' results_in growth_of some 'pollen tube' - Chris Mungall - results in growth of - - - - - - - - - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - Chris Mungall - results in transport to from or in - - - - - - - - - - - - - Chris Mungall - exports - - - - - - - - - - an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. - p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in commitment to - - - - - - - - - - p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in determination of - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - inverse of has input - Chris Mungall - - - input of - - - - - - - - - - inverse of has output - Chris Mungall - - - output of - - - - - - - - - Chris Mungall - formed as result of - - - - - - - - - - A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - Chris Mungall - results in structural organization of - - - - - - - - - - The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - Chris Mungall - http://www.geneontology.org/GO.doc.development.shtml#fate - results in specification of - - - - - - - - - p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - Chris Mungall - results in developmental induction of - - - - - - - - - Chris Mungall - http://neurolex.org/wiki/Property:DendriteLocation - has dendrite location - - - - - - - - - - - a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall - - attached to - - - - - - - - - - m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - Chris Mungall - Wikipedia:Insertion_(anatomy) - has muscle origin - - - - - - - - - - - m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - Chris Mungall - Wikipedia:Insertion_(anatomy) - has muscle insertion - - - - - - - - - - false - - x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat - Chris Mungall - Chris Mungall - - A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. - has fused element - - - - - - - - - - - - - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with - - https://github.com/obophenotype/uberon/issues/170 - - - - - - - - - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - - tributary of - - http://en.wikipedia.org/wiki/Tributary - - - - - - - - - Deschutes River distributary_of Little Lava Lake - - x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall - branch of - distributary channel of - http://en.wikipedia.org/wiki/Distributary - - This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes - distributary of - - - - - - - - - - - - - - - - - x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - Chris Mungall - anastomoses with - - anabranch of - - - - - - - - - - - - - - - A lump of clay and a statue - x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios - spatially coextensive with - - - - - - - - - - - - - - - - - - - - - - x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - Chris Mungall - - branching part of - FMA:85994 - - - - - - - - - - x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - Chris Mungall - - main stem of - - - - - - - - - - x proper_distributary_of y iff x distributary_of y and x does not flow back into y - Chris Mungall - - proper distributary of - - - - - - - - - - x proper_tributary_of y iff x tributary_of y and x does not originate from y - Chris Mungall - - proper tributary of - - - - - - - - - - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall - has developmental potential involving - - - - - - - - - - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall - has potential to developmentally contribute to - - - - - - - - - - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - Chris Mungall - has potential to developmentally induce - - - - - - - - - - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall - has potential to develop into - - - - - - - - - - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall - has potential to directly develop into - - - - - - - - - - - - - 'protein catabolic process' SubClassOf has_direct_input some protein - - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall - directly consumes - This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' - has direct input - - - - - - - - - Chris Mungall - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect input - true - - - - - - - - translation SubClassOf has_direct_output some protein - - p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. - Chris Mungall - directly produces - obsolete has direct output - true - - - - - - - - - - - - - - Chris Mungall - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - - - - - - - - - inverse of upstream of - Chris Mungall - causally downstream of - - - - - - - - - - - - Chris Mungall - immediately causally downstream of - - - - - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - directly positively regulates - - directly activates (process to process) - directly activates - - - - - - - - - - - - - - - - - - - - - - - - - - p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q - Chris Mungall - indirectly positively regulates - - indirectly activates - - - - - - - - - Chris Mungall - directly negatively regulates - - directly inhibits (process to process) - directly inhibits - - - - - - - - - - - - - - - - - - - - - - - Chris Mungall - indirectly negatively regulates - - indirectly inhibits - - - - - - - - - - This relation groups causal relations between material entities and causal relations between processes - This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. - -To define causal relations in an activity-flow type network, we make use of 3 primitives: - - * Temporal: how do the intervals of the two occurrents relate? - * Is the causal relation regulatory? - * Is the influence positive or negative - -The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. - -For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. - -For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. - -Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causally related to - - - - - - - - - - - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain - Chris Mungall - causally upstream of - - - - - - - - - - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. - Chris Mungall - - immediately causally upstream of - - - - - - - - - - - - - - - p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c - This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit - Chris Mungall - - directly provides input for (process to process) - directly provides input for - - - - - - - - - - - - - transitive form of directly_provides_input_for - Chris Mungall - This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') - transitively provides input for (process to process) - transitively provides input for - - - - - - - - - - - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. - We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall - influences (processual) - affects - causally upstream of or within - - - - - - - - false - Chris Mungall - This is an exploratory relation - differs in - https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions - - - - - - - - - - - - - - - - - Chris Mungall - differs in attribute of - - - - - - - - - - Chris Mungall - differs in attribute - - - - - - - - - - inverse of causally upstream of or within - Chris Mungall - - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some 'p' and p' regulates some p - Chris Mungall - involved in regulation of - - - - - - - - - - - - - - - - - Chris Mungall - involved in positive regulation of - - - - - - - - - - - - - - - - - Chris Mungall - involved in negative regulation of - - - - - - - - - - - c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p - Chris Mungall - involved in or reguates - involved in or involved in regulation of - - - - - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d - Chris Mungall - executes activity in - enables activity in - - - - - - - - - true - - - - - - - - - p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - Chris Mungall - contributes to morphology of - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - Considering relabeling as 'pairwise interacts with' - This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Chris Mungall - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. - in pairwise interaction with - - interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - - An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - Chris Mungall - genetically interacts with - - http://purl.obolibrary.org/obo/MI_0208 - - - - - - - - - - An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. - Chris Mungall - binds - molecularly binds with - molecularly interacts with - - http://purl.obolibrary.org/obo/MI_0915 - - - - - - - - - - - - - An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall - interacts with on organism level - - biotically interacts with - - http://eol.org/schema/terms/interactsWith - - - - - - - - - An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall - - trophically interacts with - - - - - - - - - - - A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] - Baleen whale preys on krill - An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz - is subject of predation interaction with - preys upon - - preys on - http://eol.org/schema/terms/preysUpon - http://www.inaturalist.org/observations/2942824 - - - - - - - - - - - - - - - - - A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - - - symbiotically interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - - commensually interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - - mutualistically interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - This relation groups a pair of inverse relations, parasite of and parasitized by - - - interacts with via parasite-host interaction - - - - - - - - - - - - - - - - - - Pediculus humanus capitis parasite of human - Chris Mungall - parasitizes - - direct parasite of - - parasite of - http://eol.org/schema/terms/parasitizes - - - - - - - - - - Chris Mungall - has parasite - parasitised by - directly parasitized by - - parasitized by - http://eol.org/schema/terms/hasParasite - - - - - - - - - Porifiera attaches to substrate - A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall - semibiotically interacts with - - participates in a abiotic-biotic interaction with - - - - - - - - - - - - - - - Axiomatization to GO to be added later - Chris Mungall - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. - phosphorylates - - - - - - - - - - - - - - - Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b - Chris Mungall - molecularly controls - - - - - - - - - - - - - - - - - - - Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. - Chris Mungall - inhibits - molecularly decreases activity of - - - - - - - - - - - - - - - - - - - Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. - Chris Mungall - activates - molecularly increases activity of - - - - - - - - - all dengue disease transmitted by some mosquito - A relationship that holds between a disease and organism - Add domain and range constraints - Chris Mungall - transmitted by - - - - - - - - - A relation that holds between a disease or an organism and a phenotype - Chris Mungall - has symptom - - - - - - - - - Chris Mungall - The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) - - host of - - - - - - - - - Chris Mungall - - has host - http://eol.org/schema/terms/hasHost - - - - - - - - - - Bees pollinate Flowers - This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall - is subject of pollination interaction with - - pollinates - http://eol.org/schema/terms/pollinates - - - - - - - - - Chris Mungall - has polinator - is target of pollination interaction with - - pollinated by - http://eol.org/schema/terms/hasPollinator - - - - - - - - - - Chris Mungall - Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. - - acquires nutrients from - - - - - - - - - inverse of preys on - Chris Mungall - has predator - is target of predation interaction with - - - preyed upon by - http://eol.org/schema/terms/HasPredator - http://polytraits.lifewatchgreece.eu/terms/PRED - - - - - - - - - - Anopheles is a vector for Plasmodium - Chris Mungall - a is a vector for b if a carries and transmits an infectious pathogen b into another living organism - - is vector for - - - - - - - - - Chris Mungall - - has vector - - - - - - - - - Chris Mungall - Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target - partner in - - - - - - - - - Chris Mungall - Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. - subject participant in - - - - - - - - - Chris Mungall - Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. - target participant in - - - - - - - - - Chris Mungall - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property - - - - - - - - - Chris Mungall - is symbiosis - - - - - - - - - Chris Mungall - is commensalism - - - - - - - - - Chris Mungall - is mutualism - - - - - - - - - Chris Mungall - is parasitism - - - - - - - - - Chris Mungall - - provides nutrients for - - - - - - - - - Chris Mungall - is subject of eating interaction with - - eats - - - - - - - - - Chris Mungall - eaten by - is target of eating interaction with - - is eaten by - - - - - - - - - - A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and -the a supports either the existence of b, or the truth value of b. - Chris Mungall - - is evidence for - - - - - - - - - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' - x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall - - - - composed primarily of - - - - - - - - - - - ABal nucleus child nucleus of ABa nucleus (in C elegans) - c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - Chris Mungall - This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. - child nucleus of - - - - - - - - - A child nucleus relationship in which the cells are part of a hermaphroditic organism - Chris Mungall - child nucleus of in hermaphrodite - - - - - - - - - A child nucleus relationship in which the cells are part of a male organism - Chris Mungall - child nucleus of in male - - - - - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall - - has part that occurs in - - - - - - - - - true - - - - - - - - - - - - - - An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y - Axiomatization to GO to be added later - Chris Mungall - ubiquitinates - - - - - - - - - Chris Mungall - is kinase activity - - - - - - - - - Chris Mungall - is ubiquitination - - - - - - - - - - See notes for inverse relation - Chris Mungall - receives input from - - - - - - - - - This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - Chris Mungall - sends output to - - - - - - - - - - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. - relation between structure and stage - - - - - - - - - - - - - - - - - - x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - Chris Mungall - existence starts during - - - - - - - - - x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - Chris Mungall - existence starts with - - - - - - - - - x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence overlaps - - - - - - - - - - x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts and ends during - - - - - - - - - - - - - - - - - - x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during - - - - - - - - - x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends with - - - - - - - - - - x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall - transformation of - - - - - - - - - - x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall - - immediate transformation of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts during or after - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - Chris Mungall - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during or before - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - - causal agent in - - - - - - - - - - - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between processes - - - - - - - - Chris Mungall - depends on - - - - - - - - - - q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 - This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. - Chris Mungall - - towards - - - - - - - - - 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate - p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - Chris Mungall - has intermediate product - - has intermediate - - - - - - - - - - - The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between material entities - - - - - - - - - - - - - - A coral reef environment is determined by a particular coral reef - s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. - The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall - - determined by (system to material entity) - Chris Mungall - Pier Buttigieg - - determined by - - - - - - - - - inverse of determined by - Chris Mungall - determines (material entity to system) - - - determines - - - - - - - - - - - - - - - - s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall - - determined by part of - - - - - - - - - true - - - - - - - - - - x is transcribed from y if and only if x is synthesized from template y - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - transcribed from - - - - - - - - - inverse of transcribed from - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - transcribed to - - - - - - - - - x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - ribosomal translation of - - - - - - - - - inverse of ribosomal translation of - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - ribosomally translates to - - - - - - - - - - A relation that holds between two entities that have the property of being sequences or having sequences. - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. - The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. - - sequentially related to - - - - - - - - - Every UTR is adjacent to a CDS of the same transcript - Two consecutive DNA residues are sequentially adjacent - Two exons on a processed transcript that were previously connected by an intron are adjacent - x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - sequentially adjacent to - - - - - - - - - - - Every CDS has as a start sequence the start codon for that transcript - x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - Chris Mungall - started by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has start sequence - - - - - - - - - - inverse of has start sequence - Chris Mungall - starts - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - - is start sequence of - - - - - - - - - - - Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) - x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - Chris Mungall - ended by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has end sequence - - - - - - - - - - inverse of has end sequence - Chris Mungall - ends - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - - is end sequence of - - - - - - - - - x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. - In the SO paper, this was defined as an instance-type relation - Chris Mungall - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - is consecutive sequence of - - - - - - - - - - Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. - x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - Chris Mungall - - is sequentially aligned with - - - - - - - - - - - The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) - x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - Chris Mungall - - bounds sequence of - - - - - - - - - - inverse of bounds sequence of - Chris Mungall - - - is bound by sequence of - - - - - - - - - - - - - x has subsequence y iff all of the sequence parts of x are sequence parts of y - Chris Mungall - contains - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has subsequence - - - - - - - - - - - - inverse of has subsequence - Chris Mungall - contained by - - - is subsequence of - - - - - - - - - - - - - - - x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. - Chris Mungall - - overlaps sequence of - - - - - - - - - - x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - Chris Mungall - disconnected from - - does not overlap sequence of - - - - - - - - - - inverse of downstream of sequence of - Chris Mungall - - is upstream of sequence of - - - - - - - - - - - x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - Chris Mungall - - is downstream of sequence of - - - - - - - - - - A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript - x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - Chris Mungall - - - is immediately downstream of sequence of - - - - - - - - - - A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript - inverse of immediately downstream of - Chris Mungall - - is immediately upstream of sequence of - - - - - - - - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' - A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - Chris Mungall - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - has skeleton - - - - - - - - - - p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - Chris Mungall - results in ending of - - - - - - - - - - - - - - x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y - Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall - http://eol.org/schema/terms/hyperparasitoidOf - https://en.wikipedia.org/wiki/Hyperparasite - epiparasite of - hyperparasitoid of - - hyperparasite of - - - - - - - - - - - - - inverse of hyperparasite of - Chris Mungall - has epiparasite - has hyperparasite - hyperparasitoidized by - - - hyperparasitized by - - - - - - - - - Chris Mungall - http://en.wikipedia.org/wiki/Allelopathy - - allelopath of - http://eol.org/schema/terms/allelopathyYes - x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y - - - - - - - - - - Chris Mungall - - pathogen of - - - - - - - - - Chris Mungall - - has pathogen - - - - - - - - - inverse of is evidence for - Chris Mungall - - - - x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. - has evidence - - - - - - - - - - Chris Mungall - - causally influenced by (material entity to material entity) - causally influenced by - - - - - - - - - Chris Mungall - interaction relation helper property - - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - Chris Mungall - molecular interaction relation helper property - - - - - - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - Chris Mungall - - results in movement of - - - - - - - - - - - - - - - - - - - Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b - Chris Mungall - - causally influences (material entity to material entity) - causally influences - - - - - - - - - A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. - biomechanically related to - - - - - - - - - m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - Chris Mungall - Wikipedia:Antagonist_(muscle) - has muscle antagonist - - - - - - - - - inverse of branching part of - Chris Mungall - - - has branching part - - - - - - - - - - - x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - Chris Mungall - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - - conduit for - - - - - - - - - - x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - Chris Mungall - GOC:cjm - - lumen of - - - - - - - - - - s is luminal space of x iff s is lumen_of x and s is an immaterial entity - Chris Mungall - - luminal space of - - - - - - - - - A relation that holds between an attribute or a qualifier and another attribute. - Chris Mungall - - This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. - - has modifier - - - - - - - - - Chris Mungall - - participates in a biotic-biotic interaction with - - - - - - - - - - - - inverse of has skeleton - Chris Mungall - - skeleton of - - - - - - - - - - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - Chris Mungall - - directly regulates (processual) - - directly regulates - - - - - - - - - x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. - existence starts at point - - - - - - - - - - - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' - s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall - has part structure that is capable of - - - - - - - - - - p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. - results in closure of - - - - - - - - - p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p - results in breakdown of - - - - - - - - - results in synthesis of - - - - - - - - - - results in assembly of - - - - - - - - - p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. - results in catabolism of - - - - - - - - - - results in disassembly of - - - - - - - - - - results in remodeling of - - - - - - - - - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c - results in organization of - - - - - - - - - x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. - existence ends at point - - - - - - - - - - - A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall - - causal relation between material entity and a process - - - - - - - - - - - - - pyrethroid -> growth - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - - capable of negatively regulating - - - - - - - - - - - - - renin -> arteriolar smooth muscle contraction - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - - capable of positively regulating - - - - - - - - - pazopanib -> pathological angiogenesis - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. - treats - - The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. - capable of inhibiting or preventing pathological process - - - - - treats - Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship - - - - - - - - - benzene -> cancer [CHEBI] - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. - causes disease - - capable of upregulating or causing pathological process - - - - - - - - - c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. - treats - - is substance that treats - - - - - - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - is marker for - - - - - - - - - Inverse of 'causal agent in' - - has causal agent - - - - - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - related via dependence to - - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - correlated with - - - - - - - - - An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. - A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. - In the Gene Ontology association model, this corresponds to the With/From field - is evidence with support from - - - - - - - - - Inverse of is-model-of - has model - - - - - - - - related via evidence or inference to - - - - - - - - - - visits - https://github.com/oborel/obo-relations/issues/74 - - - - - - - - - visited by - - - - - - - - - - visits flowers of - - - - - - - - - has flowers visited by - - - - - - - - - - - lays eggs in - - - - - - - - - - has eggs laid in by - - - - - - - - - - https://github.com/jhpoelen/eol-globi-data/issues/143 - kills - - - - - - - - - is killed by - - - - - - - - - - Process(P1) directly regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. - - directly positively regulates (process to process) - directly positively regulates - - - - - - - - - - Process(P1) directly regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. - - directly negatively regulates (process to process) - directly negatively regulates - - - - - - - - - - A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host - - ectoparasite of - - - - - - - - - inverse of ectoparasite of - - has ectoparasite - - - - - - - - - - - A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system - lives inside of - endoparasite of - - - - - - - - - has endoparasite - - - - - - - - - - A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite - mesoparasite of - - - - - - - - - inverse of mesoparasite of - - has mesoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. - - intercellular endoparasite of - - - - - - - - - inverse of intercellular endoparasite of - - has intercellular endoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits host cells. - - intracellular endoparasite of - - - - - - - - - inverse of intracellular endoparasite of - - has intracellular endoparasite - - - - - - - - - - - - - - - - - - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - Melissa Haendel - - Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. - produces - - - - - - - - - - - a produced_by b iff some process that occurs_in b has_output a. - Melissa Haendel - - produced by - - - - - - - - - Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. - Logical axioms to be added after the relevant branch of GO is MIREOTed in - represses expression of - - - - - - - - - Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. - Logical axioms to be added after the relevant branch of GO is MIREOTed in - increases expression of - - - - - - - - Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? - Matthew Brush - The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. - is model of - - - - - - - - - The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. - -An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. - Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - causes or contributes to condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. - causes condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. - contributes to condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. - contributes to expressivity of condition - contributes to severity of condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. - contributes to penetrance of condition - contributes to frequency of condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. - is preventative for condition - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - ameliorates condition - - - - - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - correlated with condition - - - - - - - - - A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. - exacerbates condition - - - - - - - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. - condition ameliorated by - - - - - - - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. - condition exacerbated by - - - - - - - - - - An interaction relationship wherein a plant or algae is living on the outside surface of another plant. - https://en.wikipedia.org/wiki/Epiphyte - epiphyte of - - - - - - - - - inverse of epiphyte of - - has epiphyte - - - - - - - - - - A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material - https://en.wikipedia.org/wiki/Kleptoparasitism - kleptoparasite of - - - - - - - - - inverse of kleptoparasite of - - kleptoparasitized by - - - - - - - - - An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. - creates habitat for - - - - - - - - - - An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. - co-occurs - - - - - - - - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - lays eggs on - - - - - - - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - has eggs laid on by - - - - - - - - - muffin 'has substance added' some 'baking soda' - - "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - Damion Dooley - has substance added - - - - - - - - - 'egg white' 'has substance removed' some 'egg yolk' - - "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. - Damion Dooley - has substance removed - - - - - - - - - sardines 'immersed in' some 'oil and mustard' - - "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. - Damion Dooley - immersed in - - - - - - - - - - bread 'has primary substance added' some 'flour' - - 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. - Damion Dooley - has primary substance added - - - - - - - - - - - - - - - A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. - Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. - r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte - realized in response to - https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit - - - - - - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - - ECO:0000041 - SO:similar_to - sameness - similar to - correspondence - resemblance - in similarity relationship with - - - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - BGEE:curator - - - - - correspondence - - - - - - - - - - - - - Similarity that results from common evolutionary origin. - - - homologous to - This broad definition encompasses all the working definitions proposed so far in the literature. - in homology relationship with - - - - - - Similarity that results from common evolutionary origin. - - - - - - - - - - - - - - Similarity that results from independent evolution. - - - homoplasous to - analogy - in homoplasy relationship with - - - - - - Similarity that results from independent evolution. - - - - - - - - - - - - - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - - ECO:0000075 - homocracous to - Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. - in homocracy relationship with - - - - - - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - - - - - - - - - - - - - Homoplasy that involves different underlying mechanisms or structures. - - - analogy - Convergence usually implies a notion of adaptation. - in convergence relationship with - - - - - - Homoplasy that involves different underlying mechanisms or structures. - - - - - - - - - - - - Homoplasy that involves homologous underlying mechanisms or structures. - - - parallel evolution - Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. - in parallelism relationship with - - - - - - Homoplasy that involves homologous underlying mechanisms or structures. - - - - - - - - - - - - Homology that is defined by similarity with regard to selected structural parameters. - - - ECO:0000071 - MI:2163 - structural homologous to - idealistic homology - in structural homology relationship with - - - - - - Homology that is defined by similarity with regard to selected structural parameters. - - - - ISBN:0123195837 - - - - - - - - - - Homology that is defined by common descent. - - - homology - ECO:0000080 - RO_proposed_relation:homologous_to - SO:0000330 - SO:0000853 - SO:0000857 - SO:homologous_to - TAO:homologous_to - cladistic homology - historical homologous to - phylogenetic homology - taxic homology - true homology - in historical homology relationship with - - - - - - Homology that is defined by common descent. - - - ISBN:0123195837 - - - - - - - - - - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - - ECO:0000067 - biological homologous to - transformational homology - Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. - in biological homology relationship with - - - - - - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - - - - - - - - - - - - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - - atavism - rudiment - reversion - in reversal relationship with - - - - - - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - - - - - - - - - - - Structural homology that is detected by similarity in content and organization between chromosomes. - - - MeSH:Synteny - SO:0000860 - SO:0005858 - syntenic homologous to - synteny - in syntenic homology relationship with - - - - - - Structural homology that is detected by similarity in content and organization between chromosomes. - - MeSH:Synteny - - - - - - - - - - - Historical homology that involves genes that diverged after a duplication event. - - - SO:0000854 - SO:0000859 - SO:paralogous_to - paralogous to - in paralogy relationship with - - - - - - Historical homology that involves genes that diverged after a duplication event. - - - - - - - - - - - - - - - Paralogy that involves sets of syntenic blocks. - - - syntenic paralogous to - duplicon - paralogon - in syntenic paralogy relationship with - - - - - - Paralogy that involves sets of syntenic blocks. - - - DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y - - - - - - - - - - Syntenic homology that involves chromosomes of different species. - - - syntenic orthologous to - in syntenic orthology relationship with - - - - - - Syntenic homology that involves chromosomes of different species. - - - - - - - - - - - - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - - fractional homology - partial homologous to - segmental homology - mixed homology - modular homology - partial correspondence - percent homology - in partial homology relationship with - - - - - - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - ISBN:0123195837 - ISBN:978-0471984931 - - - - - - - - - - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - - MeSH:Structural_Homology,_Protein - protein structural homologous to - in protein structural homology relationship with - - - - - - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - - - - - - - - - - - - Structural homology that involves a pseudogenic feature and its functional ancestor. - - - pseudogene - SO:non_functional_homolog_of - non functional homologous to - in non functional homology relationship with - - - - - - Structural homology that involves a pseudogenic feature and its functional ancestor. - - SO:non_functional_homolog_of - - - - - - - - - - Historical homology that involves genes that diverged after a speciation event. - - - ECO:00000060 - SO:0000855 - SO:0000858 - SO:orthologous_to - orthologous to - The term is sometimes also used for anatomical structures. - in orthology relationship with - - - - - - Historical homology that involves genes that diverged after a speciation event. - - - - - - - - - - - - - - - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - - xenologous to - The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). - in xenology relationship with - - - - - - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - - - - - - - - - - - - Historical homology that involves two members sharing no other homologs in the lineages considered. - - - 1 to 1 homologous to - 1:1 homology - one-to-one homology - in 1 to 1 homology relationship with - - - - - - Historical homology that involves two members sharing no other homologs in the lineages considered. - - BGEE:curator - - - - - - - - - - - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - - 1 to 1 orthologous to - 1:1 orthology - one-to-one orthology - in 1 to 1 orthology relationship with - - - - - - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - - - - - - - - - - - - Paralogy that results from a whole genome duplication event. - - - ohnologous to - homoeology - in ohnology relationship with - - - - - - Paralogy that results from a whole genome duplication event. - - - - - - - - - - - - - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - - in-paralogous to - inparalogy - symparalogy - in in-paralogy relationship with - - - - - - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - - - - - - - - - - - Paralogy that results from a duplication preceding a given speciation event. - - - alloparalogy - out-paralogous to - outparalogy - in out-paralogy relationship with - - - - - - Paralogy that results from a duplication preceding a given speciation event. - - - - - - - - - - - - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - - pro-orthologous to - in pro-orthology relationship with - - - - - - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - - - - - - - - - - - - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - - semi-orthologous to - The converse of pro-orthologous. - in semi-orthology relationship with - - - - - - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - - - - - - - - - - - - Iterative homology that involves structures arranged along the main body axis. - - - serial homologous to - homonomy - in serial homology relationship with - - - - - - Iterative homology that involves structures arranged along the main body axis. - - - - - - - - - - - - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - - heterochronous homologous to - heterochrony - in heterochronous homology relationship with - - - - - - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - ISBN:978-0674639416 - - - - - - - - - - - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - - juvenification - pedomorphosis - in paedomorphorsis relationship with - - - - - - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - - ISBN:978-0674639416 - - - - - - - - - - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - in peramorphosis relationship with - - - - - - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - - - - - - - - - - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - in progenesis relationship with - - - - - - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - ISBN:978-0674639416 - - - - - - - - - - Paedomorphosis that is produced by a retardation of somatic development. - - - juvenilization - neotenous to - in neoteny relationship with - - - - - - Paedomorphosis that is produced by a retardation of somatic development. - - - ISBN:978-0674639416 - - - - - - - - - - Convergence that results from co-evolution usually involving an evolutionary arms race. - - - mimicrous to - in mimicry relationship with - - - - - - Convergence that results from co-evolution usually involving an evolutionary arms race. - - - - - - - - - - - - - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - - 1 to many orthologous to - 1:many orthology - one-to-many orthology - co-orthology - many to 1 orthology - in 1 to many orthology relationship with - - - - - - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - - - - - - - - - - - - Historical homology that involves two members of a larger set of homologs. - - - many to many homologous to - many-to-many homology - many:many homology - in many to many homology relationship with - - - - - - Historical homology that involves two members of a larger set of homologs. - - - - - - - - - - - - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - - 1 to many homologous to - one-to-many homology - 1:many homology - in 1 to many homology relationship with - - - - - - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - BGEE:curator - - - - - - - - - - - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - - apomorphous to - synapomorphy - in apomorphy relationship with - - - - - - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - ISBN:978-0252068140 - - - - - - - - - - Historical homology that is based on distant shared ancestry. - - - plesiomorphous to - symplesiomorphy - This term is usually contrasted to apomorphy. - in plesiomorphy relationship with - - - - - - Historical homology that is based on distant shared ancestry. - - ISBN:978-0252068140 - - - - - - - - - - - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - - deep genetic homology - deep homologous to - generative homology - homoiology - Used for structures in distantly related taxa. - in deep homology relationship with - - - - - - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - - - - - - - - - - - - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - - hemiplasous to - in hemiplasy relationship with - - - - - - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - - - - - - - - - - - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - - gametologous to - in gametology relationship with - - - - - - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - - - - - - - - - - - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - - MeSH:Chromosome_Pairing - chromosomal homologous to - in chromosomal homology relationship with - - - - - - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - ISBN:0195307615 - - - - - - - - - - - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - - many to many orthologous to - many-to-many orthology - many:many orthology - trans-orthology - co-orthology - trans-homology - in many to many orthology relationship with - - - - - - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - - - - - - - - - - - - - Paralogy that involves genes from the same species. - - - within-species paralogous to - in within-species paralogy relationship with - - - - - - Paralogy that involves genes from the same species. - - - - - - - - - - - - Paralogy that involves genes from different species. - - - between-species paralogous to - The genes have diverged before a speciation event. - in between-species paralogy relationship with - - - - - - Paralogy that involves genes from different species. - - - - - - - - - - - - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - - post-displacement - in postdisplacement relationship with - - - - - - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - - - - - - - - - - - Peramorphosis that is produced by a delay in the offset of development. - - - in hypermorphosis relationship with - - - - - - Peramorphosis that is produced by a delay in the offset of development. - - - ISBN:978-0674639416 - - - - - - - - - - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - - synologous to - in synology relationship with - - - - - - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - - - - - - - - - - - - - Orthology that involves functional equivalent genes with retention of the ancestral function. - - - ECO:0000080 - isoorthologous to - in isoorthology relationship with - - - - - - Orthology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - - tandem paralogous to - iterative paralogy - serial paralogy - in tandem paralogy relationship with - - - - - - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - - ISBN:978-0878932665 - - - - - - - - - - - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - - apomorphic tendency - cryptic homology - latent homologous to - underlying synapomorphy - homoiology - homoplastic tendency - re-awakening - Used for structures in closely related taxa. - in latent homology relationship with - - - - - - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - - - - ISBN:0199141118 - - - - - - - - - - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - - generative homology - syngenous to - Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. - in syngeny relationship with - - - - - - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - - DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R - - - - - - - - - - - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - - 1:1 paralogy - apparent 1:1 orthology - apparent orthologous to - pseudoorthology - The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. - in apparent orthology relationship with - - - - - - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - - - - - - - - - - - - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - - pseudoparalogous to - These genes may come out as paralogs in a single-genome analysis. - in pseudoparalogy relationship with - - - - - - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - - - - - - - - - - - - Historical homology that involves functional equivalent genes with retention of the ancestral function. - - - equivalogous to - This may include examples of orthology, paralogy and xenology. - in equivalogy relationship with - - - - - - Historical homology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - - interologous to - in interology relationship with - - - - - - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - - - - - - - - - - - - Similarity that is characterized by interchangeability in function. - - - functional similarity - in functional equivalence relationship with - - - - - - Similarity that is characterized by interchangeability in function. - - - - - - - - - - - - - Biological homology that involves parts of the same organism. - - - iterative homologous to - in iterative homology relationship with - - - - - - Biological homology that involves parts of the same organism. - - - - - - - - - - - - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - - duplicate xenology - multiple xenology - paraxenologous to - in paraxenology relationship with - - - - - - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - - - - - - - - - - - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - - plerologous to - This phenomenon is usually due to gene conversion process. - in plerology relationship with - - - - - - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - - - - - - - - - - - - Structural homology that involves structures with the same or similar relative positions. - - - homotopous to - Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. - in homotopy relationship with - - - - - - Structural homology that involves structures with the same or similar relative positions. - - - - ISBN:0123195837 - - - - - - - - - - Biological homology that involves an ectopic structure and the normally positioned structure. - - - heterotopy - in homeosis relationship with - - - - - - Biological homology that involves an ectopic structure and the normally positioned structure. - - - - - - - - - - - - - - Synology that results from allopolyploidy. - - - homoeologous to - On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. - in homoeology relationship with - - - - - - Synology that results from allopolyploidy. - - - - - - - - - - - - - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - - axis paramorphism - in paramorphism relationship with - - - - - - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - - - - - - - - - - - - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - - regulogous to - in regulogy relationship with - - - - - - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - - - - - - - - - - - - - - - - - - - - - entity - - - - - - - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - continuant - - - - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. - occurrent - - - - - - - - - - - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - - - - - A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. - obsolete dependent continuant - true - - - - - - - - - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - - - - - - disposition - - - - - - - - - - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - realizable entity - - - - - - - - - quality - - - - - - - - - - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - - - - - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - role - - - - - - - - - object aggregate - - - - - - - - - site - - - - - - - - - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - generically dependent continuant - - - - - - - - - function - - - - - - - - - - - - - - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity - - - - - - - - - - - - - - - immaterial entity - - - - - - - - - - anatomical structure - - - - - - - - - - material anatomical entity - - - - - - - - - immaterial anatomical entity - - - - - - - - - - connected anatomical system - - - - - - - - - - cell part (CARO) - cell part - - - - - - - - - - multi-cell-part structure - - - - - - - - - - neuron projection bundle - - - - - - - - - Material anatomical entity that is a member of an individual species or is a viral or viroid particle. - organism or virus - Melissa Haendel - 9/18/11 - organism or virus or viroid - - - - - - - - - - - - - - - - multicellular anatomical structure - - - - - - - - - An individual member of a clade. - organism - mah - 7.16.2011 - A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. - organism - - - - - - - - - - - - - - - - cell - - - - - - - - - - neuron - - - - - - - - - macroscopic spatial feature - geographic feature - - - - - - - - - An anthropogenic geographic feature is a geographic feature -resulting from the influence of human beings on nature. - man-made feature - manmade feature - anthropogenic geographic feature - - - - - An anthropogenic geographic feature is a geographic feature -resulting from the influence of human beings on nature. - ORCID:0000-0002-4366-3088 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A feature that has been constructed by deliberate human effort. - constructed feature - construction - - - - - A feature that has been constructed by deliberate human effort. - MA:ma - - - - - - - - - biome - - - - - - - - - An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff. - mesoscopic physical object - - - - - An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff. - MA:ma - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity which determines an environmental system. - environmental feature - - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. - manufactured good - manufactured product - - - - - A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. - https://en.wikipedia.org/wiki/Manufactured_product - - - - - - - - - anthropogenic abiotic mesoscopic feature - - - - - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - portion of environmental material - environmental material - - - - - A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. - DOI:10.1186/2041-1480-4-43 - MA:ma - ORCID:0000-0002-4366-3088 - URL:http://ontology.buffalo.edu/smith/articles/niches.html - - - - - - - - - abiotic mesoscopic physical object - - - - - - - - - A system which has the disposition to environ one or more material entities. - environment - environmental system - - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anthropogenic environment is an environmental system which is the product of human activity. - anthropogenic environment - - - - - - - - - Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. - space - outer space - - - - - Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies. - https://en.wikipedia.org/wiki/Outer_space - - - - - - - - - A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. - human dwelling - - - - - A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. - https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 - - - - - - - - - An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. - celestial body - astronomical body - - - - - An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space. - https://en.wikipedia.org/wiki/Astronomical_object - - - - - - - - - - - - - - - - - - 1 - - - - An object which is composed of one or more gravitationally bound structures that are associated with a position in space. - celestial object - astronomical object - - - - - An object which is composed of one or more gravitationally bound structures that are associated with a position in space. - https://en.wikipedia.org/wiki/Astronomical_object - - - - - - - - - - - - - - - A material part of an astronomical body. - astronomical body part - - - - - - - - - - - - - - - - A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with. - biosphere - - - - - A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with. - http://www.biology-online.org/dictionary/Biosphere - https://en.wikipedia.org/wiki/Biosphere - - - - - - - - - - - - - - - - - - - - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - natural environment - - - - - An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition. - https://en.wikipedia.org/wiki/Anthropization - https://en.wikipedia.org/wiki/Natural_environment - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process during which a natural environmental system is altered by human action. - anthropization - anthropisation - - - - - A process during which a natural environmental system is altered by human action. - https://en.wikipedia.org/wiki/Anthropization - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body. - technosphere - - - - - An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body. - http://dx.doi.org/10.1177/2053019616677743 - http://www.yourdictionary.com/technosphere - https://www.sciencedaily.com/releases/2016/11/161130085021.htm - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. - manufacturing process - - - - - A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation. - https://en.wikipedia.org/wiki/Manufacturing - - - - - - - - - - - - - - - - - - - - - - - - - - An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures. - construction process - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by materials bearing roughly homogeneous qualities. - environmental system determined by a quality - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system within which an environmental material strongly influences the system's composition and properties. - environmental system determined by a material - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which is determined by a living organism. - host-associated environment - environmental system determined by an organism - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by an animal. - animal environment - Metazoan-associated environment - animal-associated environment - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead animal, or a whole small animal. - environment associated with an animal part or small animal - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system determined by part of a living or dead plant, or a whole small plant. - environment associated with a plant part or small plant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental system which includes both living and non-living components. - ecosystem + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process - + - An environmental system which includes both living and non-living components. - https://en.wikipedia.org/wiki/Ecosystem + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + - - - - - - - - - - - - - - - - - - - A process in which includes the components of an environmental system as participants. - environmental system process - - - - - - - - - - - - - - - - - - - - - - - - - - An environmental process which is driven by the action of humans. - anthropogenic environmental process - - - - - + - - - molecular process - molecular_function + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + - + - - - catalytic activity + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + - + - - - - - - true - - - ubiquitin-protein ligase activity + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + - + - - - receptor activity + + + object-aggregate + ObjectAggregate + a collection of cells in a blood biobank. + a swarm of bees is an aggregate of members who are linked together through natural bonds + a symphony orchestra + an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) + defined by fiat: the aggregate of members of an organization + defined through physical attachment: the aggregate of atoms in a lump of granite + defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container + defined via attributive delimitations such as: the patients in this hospital + the aggregate of bearings in a constant velocity axle joint + the aggregate of blood cells in your body + the nitrogen atoms in the atmosphere + the restaurants in Palo Alto + your collection of Meissen ceramic plates. + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + object aggregate + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + + + + + + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + + + + + + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + - + - - - - nucleus + + + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + site + + + + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + + + + + + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + - + - - - - The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. - behavioral response to stimulus - behaviour - behavioural response to stimulus - single-organism behavior - behavior + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant - + - The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. - GOC:ems - GOC:jl - ISBN:0395448956 - PMID:20160973 + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + - + - - - feeding behavior + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + - + - - - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - biological process - physiological process - single organism process - single-organism process - biological_process + + + immaterial + ImmaterialEntity + BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 + + immaterial entity - - - - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - GOC:go_curators - GOC:isa_complete - - + - - - - membrane + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + organism or virus + Melissa Haendel + 9/18/11 + organism or virus or viroid - + - - - - - - true - - - kinase activity + + + An individual member of a clade. + organism + mah + 7.16.2011 + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + organism - + - - - transferase activity + + + A feature that has been constructed by deliberate human effort. + "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference + constructed feature + construction + + + + A feature that has been constructed by deliberate human effort. + MA:ma + - + - - - transferase activity, transferring phosphorus-containing groups + + + A material entity which determines an environmental system. + ENVO + ENVO:00002297 + A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. + environmental feature + + + + A material entity which determines an environmental system. + DOI:10.1186/2041-1480-4-43 + NM:nm + ORCID:0000-0002-4366-3088 + - + - - - ligase activity + + + A system which has the disposition to environ one or more material entities. + 2013-09-23T16:04:08Z + EcoLexicon:environment + environment + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + A system which has the disposition to environ one or more material entities. + DOI:10.1186/2041-1480-4-43 + - + - - - ligase activity, forming carbon-nitrogen bonds + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. + Subclasses will be added by inference. + human dwelling + + + + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. + https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 + - + - - - acid-amino acid ligase activity + + + A material part of an astronomical body. + envoAstro + envoPolar + astronomical body part - + - - - small conjugating protein ligase activity + + + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. + http://orcid.org/0000-0002-4366-3088 + CMECS:577 + https://cmecscatalog.org/cmecs/classification/unit/577.html + envoCmecs + envoMarine + This class aligns to the Coastal and Marine Ecological Classification Standard (CMECS). In ENVO, we may adapt the definition for consistency, but the semantics (meaning) of the term should be unaffected. Please consult the CMECS catalogue (https://cmecscatalog.org/) for authoritative and semantically unconstrained definitions. CMECS provides the following notes: "Commonly found on intertidal mud flats along the shores of estuaries. Tidal mangrove shrublands may include immature stands or stunted mature trees that indicate a harsh growing environment. Areas characterized by tall mangroves (> 6 meters) are placed in the Tidal Mangrove Forest Biotic Group. Where tidal amplitude is relatively low, the vegetation forms narrow bands along the coastal plains, and it rarely penetrates inland more than several kilometers along rivers. Where tidal amplitude is greater, mangroves extend further inland along river courses, forming extensive stands in the major river deltas. Also, mangrove cays may occur within the lagoon complex of barrier reefs. The list of biotic communities for this group is long: a few examples are provided below, and the complete list is available in Appendix F" + tidal mangrove shrubland - + - - - - axon + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + janelomax + 2012-09-20T14:06:08Z + GO:0044708 + Wikipedia:Behavior + behavioral response to stimulus + behaviour + behavioural response to stimulus + biological_process + single-organism behavior + GO:0007610 + + + + 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. +2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). + + behavior + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. + GOC:ems + GOC:jl + ISBN:0395448956 + PMID:20160973 + - + - - - - dendrite + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + janelomax + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + + biological_process + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + @@ -11525,8 +1702,13 @@ resulting from the influence of human beings on nature. Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. + Wikipedia:Social_behavior social behaviour + biological_process cooperative behavior + GO:0035176 + Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. + social behavior @@ -11540,60 +1722,6 @@ resulting from the influence of human beings on nature. - - - - - - - - - - - - - - - presynaptic membrane - - - - - - - - - - cell projection - - - - - - - - - - neuron projection - - - - - - - - - - - - true - - - symbiosis, encompassing mutualism through parasitism - - - - @@ -11602,6 +1730,11 @@ resulting from the influence of human beings on nature. interaction with another species interspecies interaction interspecies interaction with other organisms + biological_process + GO:0044419 + + + interspecies interaction between organisms @@ -11613,77 +1746,16 @@ resulting from the influence of human beings on nature. - - - - - - synapse part - - - - - - - - - - cell part - - - - - - - - - - synapse - - - - - - - - - - - postsynaptic membrane - - - - - - - - - - - - - - - response to stimulus - - - - - - - - - interaction with symbiont - - - - Any process in which an organism has an effect on an organism of the same species. intraspecies interaction with other organisms + biological_process + GO:0051703 + + intraspecies interaction between organisms @@ -11698,11 +1770,18 @@ resulting from the influence of human beings on nature. + A biological process which involves another organism of the same or different species. + GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism + biological_process + GO:0051704 + + + multi-organism process @@ -11720,12 +1799,18 @@ resulting from the influence of human beings on nature. Any process in which an organism has a behavioral effect on another organism of the same or different species. + GO:0023032 + GO:0044709 behavioral interaction between organisms behavioral interaction with other organism behavioural interaction between organisms behavioural interaction with other organism behavioral signaling behavioral signalling + biological_process + GO:0051705 + + multi-organism behavior @@ -11743,71 +1828,6 @@ resulting from the influence of human beings on nature. - - - - - acquisition of nutrients from other organism during symbiotic interaction - - - - - - - - - - - acquisition of nutrients from symbiont - - - - - - - - - - - - true - - - parasitism - - - - - - - - - - - - true - - - mutualism - - - - - - - - - - - - true - - - commensalism - - - - @@ -11916,35 +1936,303 @@ resulting from the influence of human beings on nature. - + - - - all - root + + + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + cjm + 2018-05-20T20:55:03Z + ontology module + + + + + + + + + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + cjm + 2018-05-20T20:55:30Z + base ontology module + + + + + + + + + + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + cjm + 2018-05-20T20:55:47Z + editors ontology module + + + + + + + + + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + cjm + 2018-05-20T20:56:13Z + main release ontology module + + + + + + + + + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + cjm + 2018-05-20T20:56:23Z + bridge ontology module + + + + + + + + + + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + cjm + 2018-05-20T20:56:47Z + import ontology module + + + + + + + + + + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + cjm + 2018-05-20T20:58:11Z + subset ontology module + + + + + + + + + + + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + cjm + 2018-05-20T20:58:38Z + curation subset ontology module + + + + + + + + + An ontology module that is intended for usage in analysis or discovery applications. + cjm + 2018-05-20T20:58:49Z + analysis subset ontology module + + + + + + + + + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + cjm + 2018-05-20T20:59:19Z + single layer subset ontology module + + + + + + + + + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + cjm + 2018-05-20T20:59:57Z + exclusion subset ontology module + + + + + + + + + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + cjm + 2018-05-20T21:00:14Z + external import ontology module + + + + + + + + + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + cjm + 2018-05-20T21:14:16Z + species subset ontology module + + + + + + + + + + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + cjm + 2018-05-20T21:20:33Z + reasoned ontology module + + + + + + + + + + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + cjm + 2018-05-20T21:21:12Z + generated ontology module + + + + + + + + + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + cjm + 2018-05-20T21:21:21Z + template generated ontology module + + + + + + + + + + + + cjm + 2018-05-20T21:28:15Z + taxonomic bridge ontology module + + + + + + + + + cjm + 2018-05-22T04:15:54Z + ontology module subsetted by expressivity + + + + + + + + + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + cjm + 2018-05-22T04:16:10Z + obo basic subset ontology module + + + + + + + + + + cjm + 2018-05-22T04:16:28Z + ontology module subsetted by OWL profile + + + + + + + + + cjm + 2018-05-22T04:16:48Z + EL++ ontology module - - - - all - - - - - - all - - - + + GC_ID:1 + ncbi_taxonomy Vira Viridae viruses + Viruses @@ -11972,6 +2260,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Teleostomi @@ -11981,7 +2272,11 @@ resulting from the influence of human beings on nature. + NCBITaxon:40673 + GC_ID:1 bony vertebrates + ncbi_taxonomy + Euteleostomi @@ -11996,9 +2291,12 @@ resulting from the influence of human beings on nature. - + + GC_ID:1 + ncbi_taxonomy Viroid viroids + Viroids @@ -12020,8 +2318,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy Charophyta/Embryophyta group charophyte/embryophyte group + Streptophytina @@ -12042,8 +2344,10 @@ resulting from the influence of human beings on nature. - + GC_ID:1 + ncbi_taxonomy biota + cellular organisms @@ -12052,12 +2356,6 @@ resulting from the influence of human beings on nature. biota - - - - biota - - @@ -12065,6 +2363,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Dipnotetrapodomorpha @@ -12074,7 +2375,12 @@ resulting from the influence of human beings on nature. + GC_ID:1 + PMID:11743200 + PMID:11791233 + ncbi_taxonomy Boreotheria + Boreoeutheria @@ -12090,6 +2396,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Acrogymnospermae @@ -12099,17 +2408,49 @@ resulting from the influence of human beings on nature. + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11542017 + PMID:11542087 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:270744 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 eubacteria + ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria - not Bacteria Haeckel 1894 prokaryote prokaryotes + Bacteria + + + + prokaryotes + + @@ -12146,24 +2487,12 @@ resulting from the influence of human beings on nature. bacteria - - - - not Bacteria Haeckel 1894 - - prokaryote - - - - prokaryotes - - @@ -12171,7 +2500,11 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy Homo/Pan/Gorilla group + Homininae @@ -12187,6 +2520,34 @@ resulting from the influence of human beings on nature. + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11541975 + PMID:11542064 + PMID:11542149 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:25527841 + PMID:270744 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 + ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria @@ -12197,6 +2558,7 @@ resulting from the influence of human beings on nature. archaea prokaryote prokaryotes + Archaea @@ -12266,13 +2628,18 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + PMID:23020233 eucaryotes eukaryotes + ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes + Eukaryota @@ -12281,84 +2648,42 @@ resulting from the influence of human beings on nature. eucaryotes - - - - eucaryotes - - eukaryotes - - - - eukaryotes - - Eucarya - - - - Eucarya - - Eucaryotae - - - - Eucaryotae - - Eukarya - - - - Eukarya - - Eukaryotae - - - - Eukaryotae - - eukaryotes - - - - eukaryotes - - @@ -12366,11 +2691,16 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + PMID:23020233 green algae + ncbi_taxonomy Chlorophycota Chlorophyta sensu Bremer 1985 algae green algae + Chlorophyta @@ -12410,6 +2740,14 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + PMID:11214319 + PMID:12082125 + PMID:12878460 + PMID:15522813 + ncbi_taxonomy + Euarchontoglires @@ -12419,7 +2757,11 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy Anthropoidea + Simiiformes @@ -12435,8 +2777,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 ape apes + ncbi_taxonomy + Hominoidea @@ -12458,10 +2804,13 @@ resulting from the influence of human beings on nature. + GC_ID:1 higher plants land plants plants + ncbi_taxonomy land plants + Embryophyta @@ -12495,7 +2844,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 tetrapods + ncbi_taxonomy + Tetrapoda @@ -12511,7 +2863,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 amniotes + ncbi_taxonomy + Amniota @@ -12527,7 +2882,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 Theria + ncbi_taxonomy + Theria <Mammalia> @@ -12543,11 +2901,15 @@ resulting from the influence of human beings on nature. + + GC_ID:1 green plants + ncbi_taxonomy Chlorobionta Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants + Viridiplantae @@ -12587,8 +2949,11 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy Fungi/Metazoa group opisthokonts + Opisthokonta @@ -12610,10 +2975,14 @@ resulting from the influence of human beings on nature. + + GC_ID:1 metazoans multicellular animals + ncbi_taxonomy Animalia animals + Metazoa @@ -12647,6 +3016,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Bilateria @@ -12656,7 +3028,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 deuterostomes + ncbi_taxonomy + Deuterostomia @@ -12672,10 +3047,14 @@ resulting from the influence of human beings on nature. + GC_ID:1 + PMID:25249442 angiosperms flowering plants + ncbi_taxonomy Angiospermae flowering plants + Magnoliophyta @@ -12709,6 +3088,10 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy + Streptophyta @@ -12718,6 +3101,10 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy + Haplorrhini @@ -12727,8 +3114,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 mammals + ncbi_taxonomy mammals + Mammalia @@ -12750,8 +3141,11 @@ resulting from the influence of human beings on nature. + GC_ID:1 vascular plants + ncbi_taxonomy vascular plants + Tracheophyta @@ -12773,8 +3167,11 @@ resulting from the influence of human beings on nature. + GC_ID:1 seed plants + ncbi_taxonomy seed plants + Spermatophyta @@ -12796,6 +3193,9 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy + Eumetazoa @@ -12805,8 +3205,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 chordates + ncbi_taxonomy chordates + Chordata @@ -12828,9 +3232,12 @@ resulting from the influence of human beings on nature. + GC_ID:1 Vertebrata vertebrates + ncbi_taxonomy vertebrates + Vertebrata <Metazoa> @@ -12858,8 +3265,11 @@ resulting from the influence of human beings on nature. + GC_ID:1 Gnathostomata jawed vertebrates + ncbi_taxonomy + Gnathostomata <vertebrate> @@ -12881,7 +3291,10 @@ resulting from the influence of human beings on nature. + GC_ID:1 + ncbi_taxonomy euphyllophytes + Euphyllophyta @@ -12897,6 +3310,10 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy + Sarcopterygii @@ -12906,7 +3323,11 @@ resulting from the influence of human beings on nature. + + GC_ID:1 Craniata + ncbi_taxonomy + Craniata <chordata> @@ -12922,11 +3343,14 @@ resulting from the influence of human beings on nature. + GC_ID:1 eutherian mammals placental mammals placentals + ncbi_taxonomy Placentalia placentals + Eutheria @@ -12966,9 +3390,13 @@ resulting from the influence of human beings on nature. + + GC_ID:1 primate + ncbi_taxonomy Primata primates + Primates @@ -12996,6 +3424,10 @@ resulting from the influence of human beings on nature. + + GC_ID:1 + ncbi_taxonomy + Catarrhini @@ -13005,8 +3437,12 @@ resulting from the influence of human beings on nature. + + GC_ID:1 great apes + ncbi_taxonomy Pongidae + Hominidae @@ -13028,7 +3464,11 @@ resulting from the influence of human beings on nature. + + GC_ID:1 humans + ncbi_taxonomy + Homo @@ -13044,9 +3484,25 @@ resulting from the influence of human beings on nature. + + GC_ID:1 human man - humans + ncbi_taxonomy + Home sapiens + Homo sampiens + Homo sapeins + Homo sapian + Homo sapians + Homo sapien + Homo sapience + Homo sapiense + Homo sapients + Homo sapines + Homo spaiens + Homo spiens + Humo sapiens + Homo sapiens @@ -13061,16 +3517,96 @@ resulting from the influence of human beings on nature. man + + + + Home sapiens + + + + + + Homo sampiens + + + + + + Homo sapeins + + + + + + Homo sapian + + + + + + Homo sapians + + + + + + Homo sapien + + + + + + Homo sapience + + + + + + Homo sapiense + + + + + + Homo sapients + + + + + + Homo sapines + + + + + + Homo spaiens + + + + + + Homo spiens + + + + + + Humo sapiens + + - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - quality (PATO) + PATO:0000072 trait + quality + PATO:0000001 + quality @@ -13082,87 +3618,16 @@ resulting from the influence of human beings on nature. - - - - - A composite chromatic quality composed of hue, saturation and intensity parts. - colour - relative color - color - - - - - A composite chromatic quality composed of hue, saturation and intensity parts. - PATOC:GVG - - - - - - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - morphology - - - - - - - - - shape - - - - - - - - - qualitative - - - - - - - - - A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. - deviation(from_normal) - - - - - - - - - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. - size - - - - - - - - - structure - - - - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + rate @@ -13174,82 +3639,21 @@ resulting from the influence of human beings on nature. - - - - - A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers. - red - - - - - A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers. - Dictionary:http://dictionary.reference.com/ - - - - - - - - - branched - - - - - - - - - - A size quality which is relatively low. - hypoplasia - underdeveloped - reduced - small - tiny - decreased size - - - - - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - relational physical quality - physical quality - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATOC:GVG - - - - - - - - - linear - - - - A quality which inheres in an process. + PATO:0001239 + PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent + quality + PATO:0001236 + See comments of relational quality of a physical entity. + process quality @@ -13266,6 +3670,9 @@ resulting from the influence of human beings on nature. A quality which inheres in a continuant. + PATO:0001237 + PATO:0001238 + snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant @@ -13274,6 +3681,10 @@ resulting from the influence of human beings on nature. quality of continuant monadic quality of an object monadic quality of continuant + quality + PATO:0001241 + Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. + physical object quality @@ -13285,43 +3696,16 @@ resulting from the influence of human beings on nature. - - - - - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - electromagnetic (EM) radiation quality - - - - - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation - - - - - - - - - An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. - optical quality - - - - - An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. - PATOC:GVG - - - - A biological sex quality inhering in a population of multiple sexes. + quality + PATO:0001338 + + For example a mixture of females and male or males and hermaphrodites. + mixed sex @@ -13338,6 +3722,11 @@ resulting from the influence of human beings on nature. A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. + quality + PATO:0001415 + + + morbidity @@ -13349,27 +3738,15 @@ resulting from the influence of human beings on nature. - - - - - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. - radiation quality - - - - - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. - PATOC:GVG - - - - A quality that inheres in an entire population or part of a population. + quality + PATO:0002003 + + population quality @@ -13381,54 +3758,21 @@ resulting from the influence of human beings on nature. - - - - - branchiness - - - - + george + 2009-06-05T09:16:46Z + quality + PATO:0002062 + + physical quality of a process - - - - - laminar - - - - - - - - - A quality that has a value that is decreased compared to normal or average. - decreased quality - - - - - - - - - - A quality of an object that has a value that is decreased compared to normal or average. - decreased object quality - - - - @@ -13458,12 +3802,10 @@ resulting from the influence of human beings on nature. Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. - A material entity that consists of two or more organisms, viruses, or viroids. group of organism organism collection May be of the same or different species. collection of organisms - collection of organisms @@ -13477,7 +3819,7 @@ resulting from the influence of human beings on nature. A collection of organisms, all of the same species, that live in the same place. ISBN:0878932739 - It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. + It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population of organisms. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across OBO Foundry ontologies and only one term used. population of organisms @@ -13488,49 +3830,19 @@ Classes for population already exist in IDO ('organism population', I - + - + 2 - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - A community of at least two different species, living in a particular area. Must have at least two populations of different species as members. - Not sure if the equivalancy axiom specifies that both populations are located in the same site. + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. @@ -13870,16 +4182,14 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - A material entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. - + + + + + + + + An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. Person: Jie Zheng WEB: http://en.wikipedia.org/wiki/Household household @@ -13949,12 +4259,13 @@ Classes for population already exist in IDO ('organism population', I - - + A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. + These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). community + true @@ -13996,7 +4307,7 @@ Classes for population already exist in IDO ('organism population', I - + A material entity that is one or more organisms, viruses or viroids. organismal entity @@ -14096,7 +4407,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -14110,6 +4421,7 @@ Classes for population already exist in IDO ('organism population', I + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. pair of interacting organisms @@ -14135,6 +4447,7 @@ Classes for population already exist in IDO ('organism population', I + pair of interacting organisms of the same species @@ -14212,220 +4525,228 @@ Classes for population already exist in IDO ('organism population', I - + + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 http://orcid.org/0000-0002-4366-3088 http://dx.doi.org/10.1038/ismej.2009.88 + microbiota The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. microbial community - - - - - A plant structure (PO:0005679) which is a whole organism. - genet (broad) - ramet (broad) - planta entera (Spanish, exact) - 植物体全体 (Japanese, exact) - bush (narrow) - frutex (narrow) - frutices (narrow) - gametophyte (narrow) - herb (narrow) - liana (narrow) - prothalli (narrow) - prothallium (narrow) - prothallus (narrow) - seedling (narrow) - shrub (narrow) - sporophyte (narrow) - suffrutex (narrow) - suffrutices (narrow) - tree (narrow) - vine (narrow) - woody clump (narrow) - clonal colony (related) - colony (related) - whole plant - - - - - + - - - An anatomical structure that is or was part of a plant, or was derived from a part of a plant. - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) - plant structure + + + A material entity that is one or more organisms, viruses or viroids. + wrong IRI form + http://purl.obolibrary.org/obo/PCO_0000031 + obsolete organismal entity + true - + - - - An anatomical entity that is or was part of a plant. - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) - plant anatomical entity + + - + - - - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, - An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. - This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. - Chris Mungall - cjm - 2017-06-05T17:55:39Z - exposure event or process - https://github.com/oborel/obo-relations/pull/173 + + - + - - - - - - - - - Any entity that is ordered in discrete units along a linear axis. - Chris Mungall - sequentially ordered entity - + - + - - - Any individual unit of a collection of like units arranged in a linear order - Chris Mungall - An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. - sequence atomic unit + + + + + + + + + - + - - - Any entity that can be divided into parts such that each part is an atomical unit of a sequence - Chris Mungall - Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. - sequence bearer + + - + - - - A material entity consisting of multiple components that are causally integrated. - May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 - Chris Mungall - http://www.jbiomedsem.com/content/4/1/43 - system + + - + - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - anatomical entity + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community - + - - - A material entity that is one or more organisms, viruses or viroids. - wrong IRI form - http://purl.obolibrary.org/obo/PCO_0000031 - obsolete organismal entity - true + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye - + - - + + + + + + + + + microbial organism + microbe - + - - + + + + + + + + + + + 2 + + + + + + + + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms - + - - - Obsolete Class + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes - + - + - - - + + + + + + + + + + + 1 + + + + + + + 2 + + + - - - - - - - - - + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes - + - - + + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population @@ -14485,7 +4806,6 @@ Classes for population already exist in IDO ('organism population', I - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -14516,7 +4836,6 @@ Classes for population already exist in IDO ('organism population', I - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -14626,7 +4945,6 @@ Classes for population already exist in IDO ('organism population', I - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI @@ -14635,75 +4953,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - -## Elucidation - -This is used when the statement/axiom is assumed to hold true 'eternally' - -## How to interpret (informal) - -First the "atemporal" FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. - -## Example - - Class: nucleus - SubClassOf: part_of some cell - - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) - -## Notes - -This interpretation is *not* the same as an at-all-times relation - - - axiom holds for all times - - - - - - - - - -## Elucidation - -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. - -## Example: - - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm - - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - - - - relation has no temporal argument - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -14775,957 +4983,9 @@ binary, and takes no temporal argument. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z - contrib to MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From ligand activity to has_ligand - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From has_ligand to ligand activity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff --git a/src/ontology/reports/pco-edit.owl-obo-report.tsv b/src/ontology/reports/pco-edit.owl-obo-report.tsv new file mode 100644 index 0000000..4d1219e --- /dev/null +++ b/src/ontology/reports/pco-edit.owl-obo-report.tsv @@ -0,0 +1,24 @@ +Level Rule Name Subject Property Value +ERROR missing_label GO:0051704 rdfs:label +ERROR missing_label IAO:0000030 rdfs:label +ERROR missing_ontology_description pco.owl dc11:description +ERROR missing_ontology_license pco.owl dc:license +ERROR missing_ontology_title pco.owl dc11:title +WARN missing_definition GO:0051704 IAO:0000115 +WARN missing_definition IAO:0000030 IAO:0000115 +WARN missing_definition PCO:0000006 IAO:0000115 +WARN missing_definition PCO:0000007 IAO:0000115 +WARN missing_definition PCO:0000008 IAO:0000115 +WARN missing_definition PCO:0000014 IAO:0000115 +WARN missing_definition PCO:0000015 IAO:0000115 +WARN missing_definition PCO:0000016 IAO:0000115 +WARN missing_definition PCO:0000037 IAO:0000115 +WARN missing_definition PCO:0001001 IAO:0000115 +WARN missing_definition https://purl.obolibrary.org/obo/PCO_0000042 IAO:0000115 +WARN missing_obsolete_label PCO:0000025 rdfs:label red population@en +WARN missing_obsolete_label PCO:0000026 rdfs:label red organism@en +WARN missing_obsolete_label PCO:0000028 rdfs:label community@en +INFO missing_superclass PCO:0000003 rdfs:subClassOf +INFO missing_superclass PCO:0000004 rdfs:subClassOf +INFO missing_superclass https://purl.obolibrary.org/obo/PCO_0000043 rdfs:subClassOf +INFO missing_superclass https://purl.obolibrary.org/obo/PCO_0000045 rdfs:subClassOf