diff --git a/imports/caro_import.owl b/imports/caro_import.owl deleted file mode 100644 index c42ea9b..0000000 --- a/imports/caro_import.owl +++ /dev/null @@ -1,452 +0,0 @@ - - - - - The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. - - Common Anatomy Reference Ontology - - Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendel. - 2023-03-15 - 2023-08-15 - - - - - - - - - - - - - - - - - - - - - - - - - IAO:0000112 - uberon - example_of_usage - true - example_of_usage - example of usage - - - - - - - - definition - - - - - - - - IAO:0000116 - uberon - editor_note - true - editor_note - editor note - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - has_obo_namespace - - - - - - - - - - - - - - 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 - 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. - 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] - - - - - - - - - - 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 - 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]) - 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] - - - - - - - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CARO:0000000 - Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. - anatomical entity - - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CAROC:Brownsville2014 - - - - - - - - - An anatomical entity that has mass. - CARO:0000006 - - material anatomical entity - - - - - - - - - An anatomical structure consisting of one or more cells. - - 2018-09-28T14:20:19Z - cellular anatomical structure - - - - - - - - - Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. - Important for alignment with Darwin Core class "Organism". - biological entity - - - - - - - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. - expression pattern - - - - - - - diff --git a/imports/fbbt_import.owl b/imports/fbbt_import.owl deleted file mode 100644 index d21cf2e..0000000 --- a/imports/fbbt_import.owl +++ /dev/null @@ -1,2481 +0,0 @@ -Prefix(:=) -Prefix(owl:=) -Prefix(rdf:=) -Prefix(xml:=) -Prefix(xsd:=) -Prefix(rdfs:=) - - -Ontology( - 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-Declaration(AnnotationProperty(rdfs:comment)) -Declaration(AnnotationProperty(rdfs:label)) -Declaration(AnnotationProperty()) -############################ -# Annotation Properties -############################ - -# Annotation Property: (definition) - -AnnotationAssertion(rdfs:label "definition") - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (is a defining property chain axiom) - -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "is a defining property chain axiom") - -# Annotation Property: (is a defining property chain axiom where second argument is reflexive) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "is a defining property chain axiom where second argument is reflexive") - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (subset_property) - -AnnotationAssertion(rdfs:label "subset_property") - -# Annotation Property: (database_cross_reference) - -AnnotationAssertion(rdfs:label "database_cross_reference") - -# Annotation Property: (in_subset) - -AnnotationAssertion(rdfs:label "in_subset") - - -############################ -# Object Properties -############################ - -# Object Property: (part_of) - -AnnotationAssertion( "is part of"@en) -AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) -AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) -AnnotationAssertion( "a core relation that holds between a part and its whole"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "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'."@en) -AnnotationAssertion( "part_of"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "BFO:0000050") -AnnotationAssertion( "OBO_REL:part_of") -AnnotationAssertion( "quality") -AnnotationAssertion( "relationship") -AnnotationAssertion( "part_of") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "part_of") -AnnotationAssertion(rdfs:label "part of"@en) -AnnotationAssertion(rdfs:label "part_of") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) -AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (has part) - -AnnotationAssertion( "has part"@en) -AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) -AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) -AnnotationAssertion( "a core relation that holds between a whole and its part"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "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'."@en) -AnnotationAssertion( "has_part"@en) -AnnotationAssertion( ) -AnnotationAssertion( "BFO:0000051") -AnnotationAssertion( "OBO_REL:has_part") -AnnotationAssertion( "quality") -AnnotationAssertion( "relationship") -AnnotationAssertion( "has_part") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "has_part") -AnnotationAssertion(rdfs:label "has part"@en) -AnnotationAssertion(rdfs:label "has_part") -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (preceded by) - -AnnotationAssertion( "preceded by"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "is preceded by"@en) -AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (precedes) - -AnnotationAssertion( "precedes"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "precedes"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (characteristic_of) - -AnnotationAssertion( "inheres in"@en) -AnnotationAssertion( "this fragility is a characteristic of this vase"@en) -AnnotationAssertion( "this red color is a characteristic of this apple"@en) -AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) -AnnotationAssertion( "inheres_in"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0000052") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "characteristic_of") -AnnotationAssertion( "characteristic_of") -AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") -AnnotationAssertion(rdfs:label "characteristic of"@en) -AnnotationAssertion(rdfs:label "characteristic_of") -SubObjectPropertyOf( ) -InverseObjectProperties( ) -FunctionalObjectProperty() - -# Object Property: (has characteristic) - -AnnotationAssertion( "bearer of"@en) -AnnotationAssertion( "this apple is bearer of this red color"@en) -AnnotationAssertion( "this vase is bearer of this fragility"@en) -AnnotationAssertion( "Inverse of characteristic_of"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "bearer_of"@en) -AnnotationAssertion( "is bearer of"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0000053") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "has_characteristic") -AnnotationAssertion( "has_characteristic") -AnnotationAssertion(rdfs:label "has characteristic"@en) -AnnotationAssertion(rdfs:label "has_characteristic") -InverseFunctionalObjectProperty() -ObjectPropertyRange( ) - -# Object Property: (participates in) - -AnnotationAssertion( "participates in"@en) -AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) -AnnotationAssertion( "this input material (or this output material) participates in this process"@en) -AnnotationAssertion( "this investigator participates in this investigation"@en) -AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "participates_in"@en) -AnnotationAssertion(rdfs:label "participates in"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has participant) - -AnnotationAssertion( "has participant"@en) -AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) -AnnotationAssertion( "this investigation has participant this investigator"@en) -AnnotationAssertion( "this process has participant this input material (or this output material)"@en) -AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") -AnnotationAssertion(rdfs:label "has participant"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (function of) - -AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) -AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "function_of"@en) -AnnotationAssertion( "is function of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "function of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (quality of) - -AnnotationAssertion( "this red color is a quality of this apple"@en) -AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) -AnnotationAssertion( "is quality of"@en) -AnnotationAssertion( "quality_of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "quality of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (role of) - -AnnotationAssertion( "this investigator role is a role of this person"@en) -AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "is role of"@en) -AnnotationAssertion( "role_of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "role of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has function) - -AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "has_function"@en) -AnnotationAssertion(rdfs:label "has function"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has quality) - -AnnotationAssertion( "this apple has quality this red color"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "has_quality"@en) -AnnotationAssertion(rdfs:label "has quality"@en) -SubObjectPropertyOf( ) -ObjectPropertyRange( ) - -# Object Property: (has role) - -AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "has_role"@en) -AnnotationAssertion(rdfs:label "has role"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has disposition) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has disposition"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (disposition of) - -AnnotationAssertion( "inverse of has disposition") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "disposition of"@en) -SubObjectPropertyOf( ) - -# Object Property: (has regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has negative regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs: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'.") -AnnotationAssertion(rdfs:label "has negative regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has positive regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs: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'.") -AnnotationAssertion(rdfs:label "has positive regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has component activity) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") -AnnotationAssertion(rdfs:label "has component activity") -SubObjectPropertyOf( ) - -# Object Property: (has component process) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has component process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulated by) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( ) rdfs: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.") -AnnotationAssertion(rdfs:label "directly regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly negatively regulated by) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly negatively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly positively regulated by) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly positively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has effector activity) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") -AnnotationAssertion(rdfs:label "has effector activity") -SubObjectPropertyOf( ) -FunctionalObjectProperty() - -# Object Property: (ends after) - -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) -AnnotationAssertion(rdfs:label "ends after"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately preceded by) - -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "starts_at_end_of") -AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately precedes) - -AnnotationAssertion( ) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "ends_at_start_of") -AnnotationAssertion( "meets") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately precedes"@en) -SubObjectPropertyOf( ) - -# Object Property: (overlaps) - -AnnotationAssertion( ) -AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") -AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002131") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "overlaps") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "overlaps") -AnnotationAssertion(rdfs:label "overlaps"@en) -AnnotationAssertion(rdfs:label "overlaps") -SubObjectPropertyOf( ) -SymmetricObjectProperty() - -# Object Property: (has component) - -AnnotationAssertion( ) -AnnotationAssertion( "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.") -AnnotationAssertion( "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.") -AnnotationAssertion( "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."@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has component"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (expressed in) - -AnnotationAssertion( "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'") -AnnotationAssertion( ) -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "expressed in"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyDomain( ObjectUnionOf( )) - -# Object Property: (regulates) - -AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "GO") -AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") -AnnotationAssertion( "regulates (processual)") -AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion( "RO:0002211") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulates) - -AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "negatively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002212") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "negatively_regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (positively regulates) - -AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "positively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002213") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "positively_regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (capable_of) - -AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") -AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") -AnnotationAssertion( "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. ") -AnnotationAssertion( ) -AnnotationAssertion( "has function realized in") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "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)\".") -AnnotationAssertion( "RO:0002215") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "capable_of") -AnnotationAssertion( ) -AnnotationAssertion( "capable_of") -AnnotationAssertion(rdfs:label "capable of"@en) -AnnotationAssertion(rdfs:label "capable_of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable_of_part_of) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "has function in") -AnnotationAssertion( "RO:0002216") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "capable_of_part_of") -AnnotationAssertion( "capable_of_part_of") -AnnotationAssertion(rdfs:label "capable of part of"@en) -AnnotationAssertion(rdfs:label "capable_of_part_of") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (temporally related to) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "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.") -AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") -AnnotationAssertion(rdfs:label "temporally related to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has input) - -AnnotationAssertion( ) -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "consumes") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has input"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (acts upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within) - -AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") -AnnotationAssertion( "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.") -AnnotationAssertion( "affects") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (expresses) - -AnnotationAssertion( ) -AnnotationAssertion( "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002292") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "expresses") -AnnotationAssertion( "expresses") -AnnotationAssertion(rdfs:label "expresses"@en) -AnnotationAssertion(rdfs:label "expresses") -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of, positive effect) - -AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs: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") -AnnotationAssertion(rdfs:label "causally upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of, negative effect) - -AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (characteristic of part of) - -AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") -AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of") -AnnotationAssertion( ) -AnnotationAssertion( "inheres in part of") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "characteristic of part of"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (mereotopologically related to) - -AnnotationAssertion( "A mereological relationship or a topological relationship") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "mereotopologically related to"@en) - -# Object Property: (enables) - -AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") -AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") -AnnotationAssertion( ) -AnnotationAssertion( "catalyzes") -AnnotationAssertion( "executes") -AnnotationAssertion( "has") -AnnotationAssertion( "is catalyzing") -AnnotationAssertion( "is executing") -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enables"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (functionally related to) - -AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") -AnnotationAssertion( ) -AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") -AnnotationAssertion(rdfs:label "functionally related to"@en) - -# Object Property: (part of structure that is capable of) - -AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") -AnnotationAssertion( ) -AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) -SubObjectPropertyOf( ) - -# Object Property: (genomically related to) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "genomically related to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (involved in) - -AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") -AnnotationAssertion( ) -AnnotationAssertion( "actively involved in") -AnnotationAssertion( "enables part of") -AnnotationAssertion(rdfs:label "involved in"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enabled by) - -AnnotationAssertion( "inverse of enables") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enabled by"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (regulated by) - -AnnotationAssertion( "inverse of regulates") -AnnotationAssertion( ) -AnnotationAssertion( "regulated by (processual)") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulated by"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulated by) - -AnnotationAssertion( "inverse of negatively regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (positively regulated by) - -AnnotationAssertion( "inverse of positively regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (input of) - -AnnotationAssertion( "inverse of has input") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "input of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally downstream of) - -AnnotationAssertion( ) -AnnotationAssertion( "inverse of upstream of") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately causally downstream of) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (indirectly positively regulates) - -AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly activates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (indirectly negatively regulates) - -AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly inhibits") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (causally related to) - -AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causally related to"@en) - -# Object Property: (causally upstream of) - -AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately causally upstream of) - -AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within) - -AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") -AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") -AnnotationAssertion( ) -AnnotationAssertion( "influences (processual)") -AnnotationAssertion( "affects") -AnnotationAssertion(rdfs:label "causally upstream of or within") -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (causally downstream of or within) - -AnnotationAssertion( "inverse of causally upstream of or within") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally downstream of or within") -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (involved in regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (involved in positive regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in positive regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in negative regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in negative regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in or involved in regulation of) - -AnnotationAssertion( "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") -AnnotationAssertion( "OWL does not allow defining object properties via a Union") -AnnotationAssertion( ) -AnnotationAssertion( "involved in or reguates") -AnnotationAssertion(rdfs:label "involved in or involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (interacts with) - -AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "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.") -AnnotationAssertion( "in pairwise interaction with") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interacts with") -AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) -SymmetricObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (molecularly interacts with) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "binds") -AnnotationAssertion( "molecularly binds with") -AnnotationAssertion(rdfs:label "molecularly interacts with") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) -SubObjectPropertyOf( ) -SymmetricObjectProperty() - -# Object Property: (phosphorylates) - -AnnotationAssertion( "Axiomatization to GO to be added later") -AnnotationAssertion( ) -AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") -AnnotationAssertion(rdfs:label "phosphorylates") -SubObjectPropertyOf( ) - -# Object Property: (directly regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "molecularly controls") -AnnotationAssertion(rdfs:label "directly regulates activity of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly negatively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly inhibits") -AnnotationAssertion( "molecularly decreases activity of") -AnnotationAssertion(rdfs:label "directly negatively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly positively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly activates") -AnnotationAssertion( "molecularly increases activity of") -AnnotationAssertion(rdfs:label "directly positively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (helper property (not for use in curation)) - -AnnotationAssertion( ) -AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") -AnnotationAssertion(rdfs:label "helper property (not for use in curation)") - -# Object Property: (is kinase activity) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "is kinase activity") -SubObjectPropertyOf( ) - -# Object Property: (causal agent in process) - -AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causal agent in process") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (causal relation between processes) - -AnnotationAssertion( "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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causal relation between processes") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (depends on) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "depends on") -AnnotationAssertion(rdfs:seeAlso ) - -# Object Property: (causal relation between entities) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causal relation between entities") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (causally influenced by) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influenced by (entity-centric)") -AnnotationAssertion(rdfs:label "causally influenced by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (interaction relation helper property) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interaction relation helper property") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (molecular interaction relation helper property) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "molecular interaction relation helper property") -SubObjectPropertyOf( ) - -# Object Property: (causally influences) - -AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influences (entity-centric)") -AnnotationAssertion(rdfs:label "causally influences") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulates) - -AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly regulates (processual)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has part structure that is capable of) - -AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has part structure that is capable of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causal relation between material entity and a process) - -AnnotationAssertion( "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.") -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causal relation between material entity and a process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of regulating) - -AnnotationAssertion( "pyrethroid -> growth") -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of negatively regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of negatively regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of positively regulating) - -AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of positively regulating") -SubObjectPropertyOf( ) - -# Object Property: (process has causal agent) - -AnnotationAssertion( "Inverse of 'causal agent in process'") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "process has causal agent") -SubObjectPropertyOf( ) - -# Object Property: (correlated with) - -AnnotationAssertion( "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.") -AnnotationAssertion( "Groups both positive and negative correlation") -AnnotationAssertion(rdfs:label "correlated with") - -# Object Property: (directly positively regulates) - -AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly positively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly positively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (directly negatively regulates) - -AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly negatively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly negatively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enables subfunction) - -AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "enables subfunction") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, positive effect) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, negative effect) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (regulates activity of) - -AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (indirectly causally upstream of) - -AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) -SubObjectPropertyOf( ) - -# Object Property: (indirectly regulates) - -AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (device utilizes material) - -AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") -AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") -AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( "2021-11-08T12:00:00Z") -AnnotationAssertion( "utilizes") -AnnotationAssertion(rdfs:label "device utilizes material"@en) - -# Object Property: (positively correlated with) - -AnnotationAssertion( "A relation between entities in which one increases or decreases as the other does the same."@en) -AnnotationAssertion( "directly correlated with"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively correlated with"@en) -SubObjectPropertyOf( ) -SymmetricObjectProperty() -ReflexiveObjectProperty() - -# Object Property: (regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates characteristic") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (positively regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulates characteristic") -SubObjectPropertyOf( ) - -# Object Property: (negatively regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulates characteristic") -SubObjectPropertyOf( ) - - - -############################ -# Classes -############################ - -# Class: (continuant) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (occurrent) - -AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) -AnnotationAssertion(rdfs:label "occurrent"@en) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (independent continuant) - -AnnotationAssertion( "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])"@en) -AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) -AnnotationAssertion(rdfs:label "independent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (process) - -AnnotationAssertion( "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])"@en) -AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) -AnnotationAssertion(rdfs:label "process"@en) -SubClassOf( ) - -# Class: (disposition) - -AnnotationAssertion(rdfs:label "disposition"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (realizable entity) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "realizable entity"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (quality) - -AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (specifically dependent continuant) - -AnnotationAssertion( "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])"@en) -AnnotationAssertion(rdfs:comment "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."@en) -AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (role) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "role"@en) -SubClassOf( ) - -# Class: (generically dependent continuant) - -AnnotationAssertion( "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])"@en) -AnnotationAssertion(rdfs:comment "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."@en) -AnnotationAssertion(rdfs:label "generically dependent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (function) - -AnnotationAssertion(rdfs:label "function"@en) -SubClassOf( ) - -# Class: (material entity) - -AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) -AnnotationAssertion(rdfs:label "material entity"@en) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (immaterial entity) - -AnnotationAssertion(rdfs:label "immaterial entity"@en) -SubClassOf( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (anatomical entity) - -AnnotationAssertion(Annotation( "CAROC:Brownsville2014") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") -AnnotationAssertion( "CARO:0000000") -AnnotationAssertion(rdfs:comment "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.") -AnnotationAssertion(rdfs:label "anatomical entity") -SubClassOf( ) -DisjointUnion( ) - -# Class: (material anatomical entity) - -AnnotationAssertion( "An anatomical entity that has mass.") -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "material anatomical entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (immaterial anatomical entity) - -AnnotationAssertion( "Anatomical entity that has no mass.") -AnnotationAssertion( "CARO:0000007") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immaterial anatomical entity") -EquivalentClasses( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))) -SubClassOf( ) -SubClassOf( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (biological entity) - -AnnotationAssertion( "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.") -AnnotationAssertion(rdfs:comment "Important for alignment with Darwin Core class \"Organism\".") -AnnotationAssertion(rdfs:label "biological entity") -SubClassOf( ) - -# Class: (anatomical structure) - -AnnotationAssertion(Annotation( "CARO:MAH") Annotation( "FBC:DOS") "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.") -AnnotationAssertion( "CARO:0000003") -AnnotationAssertion( "UBERON:0000061") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "FBbt:00007001") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anatomical structure") -SubClassOf( ) - -# Class: (material anatomical entity) - -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion( "UBERON:0000465") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "FBbt:00007016") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "material anatomical entity") -SubClassOf( ) - -# Class: (multicellular structure) - -AnnotationAssertion(Annotation( "FBC:DOS") "Anatomical structure that has multiple cells as parts.") -AnnotationAssertion( ) -AnnotationAssertion( "2010-11-02T02:25:04Z"^^xsd:dateTime) -AnnotationAssertion( "UBERON:0010000") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "FBbt:00100313") -AnnotationAssertion(rdfs:label "multicellular structure") -SubClassOf( ) - -# Class: (anatomical entity) - -AnnotationAssertion(Annotation( "CARO:MAH") "Anatomical entity which is part_of Drosophila melanogaster.") -AnnotationAssertion( "FBbt_root:00000000") -AnnotationAssertion( "UBERON:0001062") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "Drosophila") -AnnotationAssertion( "FBbt:10000000") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anatomical entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -DisjointClasses( ) - -# Class: (molecular_function) - -AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") -AnnotationAssertion( "GO:0005554") -AnnotationAssertion( "molecular function") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0003674") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") -AnnotationAssertion(rdfs:label "molecular_function") - -# Class: (catalytic activity) - -AnnotationAssertion(Annotation( "GOC:vw") Annotation( "ISBN:0198506732") "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.") -AnnotationAssertion( "Wikipedia:Enzyme") -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "enzyme activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0003824") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "catalytic activity") -SubClassOf( ) - -# Class: (biological_process) - -AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24968"^^xsd:anyURI) -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-09-19T15:05:24Z") -AnnotationAssertion( "GO:0000004") -AnnotationAssertion( "GO:0007582") -AnnotationAssertion( "GO:0044699") -AnnotationAssertion( "Wikipedia:Biological_process") -AnnotationAssertion( "biological process") -AnnotationAssertion( "physiological process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "single organism process") -AnnotationAssertion( "single-organism process") -AnnotationAssertion( "GO:0008150") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs: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.") -AnnotationAssertion(rdfs:label "biological_process") - -# Class: (kinase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") -AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") -AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") -AnnotationAssertion( "phosphokinase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016301") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") -AnnotationAssertion(rdfs:label "kinase activity") -SubClassOf( ) -SubClassOf( ObjectHasSelf()) - -# Class: (transferase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") -AnnotationAssertion( "EC:2.-.-.-") -AnnotationAssertion(Annotation(rdfs:label "PE is converted to PS by PTDSS2") "Reactome:R-HSA-1483089") -AnnotationAssertion(Annotation(rdfs:label "PC is converted to PS by PTDSS1") "Reactome:R-HSA-1483186") -AnnotationAssertion(Annotation(rdfs:label "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK") "Reactome:R-HSA-5668414") -AnnotationAssertion(Annotation(rdfs:label "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248") "Reactome:R-HSA-8868783") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016740") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "transferase activity") -SubClassOf( ) - -# Class: (transferase activity, transferring phosphorus-containing groups) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") -AnnotationAssertion( "EC:2.7.-.-") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016772") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.") -AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups") -SubClassOf( ) - -# Class: (root) - -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "all") -AnnotationAssertion( "NCBITaxon:1") -AnnotationAssertion(rdfs:label "root") - -# Class: (Ecdysozoa) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:1206794") -AnnotationAssertion(rdfs:label "Ecdysozoa") -SubClassOf( ) - -# Class: (cellular organisms) - -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "biota") -AnnotationAssertion( "NCBITaxon:131567") -AnnotationAssertion(rdfs:label "cellular organisms") -SubClassOf( ) - -# Class: (Pancrustacea) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "PMID:10874751") -AnnotationAssertion( "PMID:11557979") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:197562") -AnnotationAssertion(rdfs:label "Pancrustacea") -SubClassOf( ) - -# Class: (Mandibulata) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "PMID:11557979") -AnnotationAssertion( "PMID:9727836") -AnnotationAssertion(Annotation( ) "mandibulates") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:197563") -AnnotationAssertion(rdfs:label "Mandibulata") -SubClassOf( ) - -# Class: (Eukaryota) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "PMID:23020233") -AnnotationAssertion( "PMID:30257078") -AnnotationAssertion(Annotation( ) "eucaryotes") -AnnotationAssertion(Annotation( ) "eukaryotes") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Eucarya") -AnnotationAssertion(Annotation( ) "Eucaryotae") -AnnotationAssertion(Annotation( ) "Eukarya") -AnnotationAssertion(Annotation( ) "Eukaryotae") -AnnotationAssertion(Annotation( ) "eukaryotes") -AnnotationAssertion( "NCBITaxon:2759") -AnnotationAssertion(rdfs:label "Eukaryota") -SubClassOf( ) - -# Class: (Sophophora) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:32341") -AnnotationAssertion(rdfs:label "Sophophora") -SubClassOf( ) - -# Class: (melanogaster group) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:32346") -AnnotationAssertion(rdfs:label "melanogaster group") -SubClassOf( ) - -# Class: (melanogaster subgroup) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:32351") -AnnotationAssertion(rdfs:label "melanogaster subgroup") -SubClassOf( ) - -# Class: (Opisthokonta) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Fungi/Metazoa group") -AnnotationAssertion(Annotation( ) "opisthokonts") -AnnotationAssertion( "NCBITaxon:33154") -AnnotationAssertion(rdfs:label "Opisthokonta") -SubClassOf( ) - -# Class: (Metazoa) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "metazoans") -AnnotationAssertion(Annotation( ) "multicellular animals") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Animalia") -AnnotationAssertion(Annotation( ) "animals") -AnnotationAssertion( "NCBITaxon:33208") -AnnotationAssertion(rdfs:label "Metazoa") -SubClassOf( ) - -# Class: (Bilateria) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:33213") -AnnotationAssertion(rdfs:label "Bilateria") -SubClassOf( ) - -# Class: (Protostomia) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:33317") -AnnotationAssertion(rdfs:label "Protostomia") -SubClassOf( ) - -# Class: (Neoptera) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:33340") -AnnotationAssertion(rdfs:label "Neoptera") -SubClassOf( ) - -# Class: (Endopterygota) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Holometabola") -AnnotationAssertion( "NCBITaxon:33392") -AnnotationAssertion(rdfs:label "Endopterygota") -SubClassOf( ) - -# Class: (Muscomorpha) - -AnnotationAssertion( ) -AnnotationAssertion( "NCBITaxon:43732") -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Asilomorpha") -AnnotationAssertion( "NCBITaxon:43733") -AnnotationAssertion(rdfs:label "Muscomorpha") -SubClassOf( ) - -# Class: (Schizophora) - -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:43738") -AnnotationAssertion(rdfs:label "Schizophora") -SubClassOf( ) - -# Class: (Acalyptratae) - -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:43741") -AnnotationAssertion(rdfs:label "Acalyptratae") -SubClassOf( ) - -# Class: (Ephydroidea) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:43746") -AnnotationAssertion(rdfs:label "Ephydroidea") -SubClassOf( ) - -# Class: (Drosophilinae) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:43845") -AnnotationAssertion(rdfs:label "Drosophilinae") -SubClassOf( ) - -# Class: (Drosophilini) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:46877") -AnnotationAssertion(rdfs:label "Drosophilini") -SubClassOf( ) - -# Class: (Cyclorrhapha) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:480117") -AnnotationAssertion(rdfs:label "Cyclorrhapha") -SubClassOf( ) - -# Class: (Eremoneura) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:480118") -AnnotationAssertion(rdfs:label "Eremoneura") -SubClassOf( ) - -# Class: (Insecta) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "true insects") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "insects") -AnnotationAssertion( "NCBITaxon:50557") -AnnotationAssertion(rdfs:label "Insecta") -SubClassOf( ) - -# Class: (Eumetazoa) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:6072") -AnnotationAssertion(rdfs:label "Eumetazoa") -SubClassOf( ) - -# Class: (Arthropoda) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "arthropods") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "arthropods") -AnnotationAssertion( "NCBITaxon:6656") -AnnotationAssertion(rdfs:label "Arthropoda") -SubClassOf( ) - -# Class: (Hexapoda) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "insects") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Atelocerata") -AnnotationAssertion(Annotation( ) "Tracheata") -AnnotationAssertion(Annotation( ) "Uniramia") -AnnotationAssertion(Annotation( ) "hexapods") -AnnotationAssertion( "NCBITaxon:6960") -AnnotationAssertion(rdfs:label "Hexapoda") -SubClassOf( ) - -# Class: (Diptera) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "flies") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "flies") -AnnotationAssertion( "NCBITaxon:7147") -AnnotationAssertion(rdfs:label "Diptera") -SubClassOf( ) - -# Class: (Brachycera) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:7203") -AnnotationAssertion(rdfs:label "Brachycera") -SubClassOf( ) - -# Class: (Drosophilidae) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "pomace flies") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:7214") -AnnotationAssertion(rdfs:label "Drosophilidae") -SubClassOf( ) - -# Class: (Drosophila ) - -AnnotationAssertion( ) -AnnotationAssertion( "NCBITaxon:7326") -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "Drosophila") -AnnotationAssertion(Annotation( ) "fruit flies") -AnnotationAssertion(Annotation( ) "fruit fly") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:7215") -AnnotationAssertion(rdfs:label "Drosophila ") -SubClassOf( ) - -# Class: (Drosophila melanogaster) - -AnnotationAssertion( ) -AnnotationAssertion( "NCBITaxon:2267365") -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "fruit fly") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Sophophora melanogaster") -AnnotationAssertion( "NCBITaxon:7227") -AnnotationAssertion(rdfs:label "Drosophila melanogaster") -SubClassOf( ) - -# Class: (Pterygota ) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "Pterygota") -AnnotationAssertion(Annotation( ) "winged insects") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:7496") -AnnotationAssertion(rdfs:label "Pterygota ") -SubClassOf( ) - -# Class: (Dicondylia) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:85512") -AnnotationAssertion(rdfs:label "Dicondylia") -SubClassOf( ) - -# Class: (Panarthropoda) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:88770") -AnnotationAssertion(rdfs:label "Panarthropoda") -SubClassOf( ) - -# Class: (quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") -AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.") -AnnotationAssertion( "PATO:0000072") -AnnotationAssertion( "trait") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0000001") -AnnotationAssertion(rdfs:label "quality") - -# Class: (mass) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0000125") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism.") -AnnotationAssertion(rdfs:label "mass") -SubClassOf( ) - -# Class: (physical quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.") -AnnotationAssertion( "PATO:0002079") -AnnotationAssertion( "Wikipedia:Physical_property") -AnnotationAssertion( "relational physical quality") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0001018") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "physical quality") -SubClassOf( ) - -# Class: (physical object quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A quality which inheres in a continuant.") -AnnotationAssertion( "PATO:0001237") -AnnotationAssertion( "PATO:0001238") -AnnotationAssertion( "snap:Quality") -AnnotationAssertion( "monadic quality of a continuant") -AnnotationAssertion( "multiply inhering quality of a physical entity") -AnnotationAssertion( "multiply inhering quality of a physical entity ") -AnnotationAssertion( "quality of a continuant") -AnnotationAssertion( "quality of a single physical entity") -AnnotationAssertion( "quality of an object") -AnnotationAssertion( "quality of continuant") -AnnotationAssertion( "monadic quality of an object") -AnnotationAssertion( "monadic quality of continuant") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0001241") -AnnotationAssertion(rdfs: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.") -AnnotationAssertion(rdfs:label "physical object quality") -SubClassOf( ) - - -EquivalentClasses(Annotation(rdfs:comment "Should belong in BFO, but lives in caro for now.") ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(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") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "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'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(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'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -) \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/imports/merged_import.owl similarity index 73% rename from src/ontology/imports/ro_import.owl rename to imports/merged_import.owl index ca7276c..c2ad10e 100644 --- a/src/ontology/imports/ro_import.owl +++ b/imports/merged_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,9 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-08-15") +Ontology( + +Annotation(owl:versionInfo "2023-10-26") Declaration(Class()) Declaration(Class()) @@ -23,22 +22,68 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -125,9 +170,9 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -135,24 +180,16 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -162,11 +199,13 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -179,19 +218,19 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -200,50 +239,24 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(Datatype(xsd:date)) ############################ # Annotation Properties ############################ # Annotation Property: (definition) -AnnotationAssertion( "definition"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) -AnnotationAssertion( "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. "@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") # Annotation Property: () @@ -276,17 +289,29 @@ SubAnnotationPropertyOf( < SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: () -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () -# Annotation Property: () +SubAnnotationPropertyOf( ) -SubAnnotationPropertyOf( ) +# Annotation Property: () -# Annotation Property: () +SubAnnotationPropertyOf( ) -SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) # Annotation Property: (subset_property) @@ -360,6 +385,35 @@ AnnotationAssertion(rdfs:label "has SubObjectPropertyOf( ) TransitiveObjectProperty() +# Object Property: (realized in) + +AnnotationAssertion( "realized in"@en) +AnnotationAssertion( "this disease is realized in this disease course"@en) +AnnotationAssertion( "this fragility is realized in this shattering"@en) +AnnotationAssertion( "this investigator role is realized in this investigation"@en) +AnnotationAssertion( "is realized by"@en) +AnnotationAssertion( "realized_in"@en) +AnnotationAssertion( "[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])"@en) +AnnotationAssertion(rdfs:comment "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") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realized in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (realizes) + +AnnotationAssertion( "realizes"@en) +AnnotationAssertion( "this disease course realizes this disease"@en) +AnnotationAssertion( "this investigation realizes this investigator role"@en) +AnnotationAssertion( "this shattering realizes this fragility"@en) +AnnotationAssertion( "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])"@en) +AnnotationAssertion(rdfs:comment "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") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (preceded by) AnnotationAssertion( "preceded by"@en) @@ -367,7 +421,7 @@ AnnotationAssertion( "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."@en) AnnotationAssertion( "is preceded by"@en) AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "preceded by"@en) SubObjectPropertyOf( ) @@ -387,6 +441,72 @@ TransitiveObjectProperty() ObjectPropertyDomain( ) ObjectPropertyRange( ) +# Object Property: (has_specified_input) + +AnnotationAssertion( "has_specified_input"@en) +AnnotationAssertion( "has_specified_input") +AnnotationAssertion( "see is_input_of example_of_usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_input_of"@en) +AnnotationAssertion( "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Coutot") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has_specified_input"@en) +EquivalentObjectProperties( ObjectInverseOf()) +SubObjectPropertyOf( ) + +# Object Property: (is_specified_input_of) + +AnnotationAssertion( "is_specified_input_of") +AnnotationAssertion( "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "is_specified_input_of"@en) +SubObjectPropertyOf( ) + +# Object Property: (has_specified_output) + +AnnotationAssertion( "has_specified_output"@en) +AnnotationAssertion( "has_specified_output") +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_output_of"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has_specified_output"@en) +EquivalentObjectProperties( ObjectInverseOf()) +SubObjectPropertyOf( ) + +# Object Property: (is_specified_output_of) + +AnnotationAssertion( "is_specified_output_of"@en) +AnnotationAssertion( "is_specified_output_of") +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "is_specified_output_of"@en) +SubObjectPropertyOf( ) + +# Object Property: (achieves_planned_objective) + +AnnotationAssertion( "achieves_planned_objective") +AnnotationAssertion( "A cell sorting process achieves the objective specification 'material separation objective'") +AnnotationAssertion( ) +AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.") +AnnotationAssertion( "BP, AR, PPPB branch") +AnnotationAssertion( "PPPB branch derived") +AnnotationAssertion( "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch") +AnnotationAssertion(rdfs:label "achieves_planned_objective") + # Object Property: (characteristic of) AnnotationAssertion( "inheres in"@en) @@ -437,11 +557,30 @@ AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion( "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."@en) AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) +# Object Property: (is concretized as) + +AnnotationAssertion( "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)."@en) +AnnotationAssertion( "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)."@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion(rdfs:label "is concretized as"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (concretizes) + +AnnotationAssertion( "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)."@en) +AnnotationAssertion( "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)."@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion(rdfs:label "concretizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (function of) AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) @@ -1362,12 +1501,6 @@ AnnotationAssertion( "process has causal agent") SubObjectPropertyOf( ) -# Object Property: (correlated with) - -AnnotationAssertion( "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.") -AnnotationAssertion( "Groups both positive and negative correlation") -AnnotationAssertion(rdfs:label "correlated with") - # Object Property: (directly positively regulates) AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") @@ -1396,6 +1529,16 @@ AnnotationAssertion(rdfs:seeAlso "ht SubObjectPropertyOf( ) SubObjectPropertyOf( ) +# Object Property: (realized in response to stimulus) + +AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-12-26T19:45:49Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "realized in response to stimulus") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (enables subfunction) AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") @@ -1466,6 +1609,49 @@ AnnotationAssertion(rdfs:label "caus AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) +# Object Property: (realized in response to) + +AnnotationAssertion( "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.") +AnnotationAssertion( "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") +AnnotationAssertion( "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.") +AnnotationAssertion( "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.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "triggered by process") +AnnotationAssertion(rdfs:label "realized in response to"@en) +AnnotationAssertion(rdfs:seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (generically depends on) + +AnnotationAssertion( "Genetic information generically depend on molecules of DNA.") +AnnotationAssertion( "The novel *War and Peace* generically depends on this copy of the novel.") +AnnotationAssertion( "The pattern shared by chess boards generically depends on any chess board.") +AnnotationAssertion( "The score of a symphony g-depends on a copy of the score.") +AnnotationAssertion( "This pdf file generically depends on this server.") +AnnotationAssertion( "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion( "g-depends on") +AnnotationAssertion(rdfs:label "generically depends on") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is carrier of) + +AnnotationAssertion( "Molecules of DNA are carriers of genetic information.") +AnnotationAssertion( "This copy of *War and Peace* is carrier of the novel written by Tolstoy.") +AnnotationAssertion( "This hard drive is carrier of these data items.") +AnnotationAssertion( "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion(rdfs:label "is carrier of"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (regulates activity of) AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") @@ -1500,20 +1686,10 @@ AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( "2021-11-08T12:00:00Z") +AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) -# Object Property: (positively correlated with) - -AnnotationAssertion( "A relation between entities in which one increases or decreases as the other does the same."@en) -AnnotationAssertion( "directly correlated with"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively correlated with"@en) -SubObjectPropertyOf( ) -SymmetricObjectProperty() -ReflexiveObjectProperty() - # Object Property: (regulates characteristic) AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") @@ -1628,190 +1804,407 @@ SubClassOf( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) AnnotationAssertion(rdfs:label "material entity"@en) SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (immaterial entity) + +AnnotationAssertion(rdfs:label "immaterial entity"@en) +SubClassOf( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (anatomical entity) + +AnnotationAssertion(Annotation( "CAROC:Brownsville2014") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion( "CARO:0000000") +AnnotationAssertion(rdfs:comment "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.") +AnnotationAssertion(rdfs:label "anatomical entity") +SubClassOf( ) + +# Class: (connected anatomical structure) + +AnnotationAssertion( "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.") +AnnotationAssertion( "CARO:0000003") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.") +AnnotationAssertion(rdfs:label "connected anatomical structure") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organism substance) + +AnnotationAssertion( "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle.") +AnnotationAssertion( "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome.") +AnnotationAssertion( "portion of organism substance") +AnnotationAssertion( "CARO:0000004") +AnnotationAssertion(rdfs:comment "Note - CARO explicitly declares organisms substances to be part of (some) organism.") +AnnotationAssertion(rdfs:label "organism substance") +SubClassOf( ) + +# Class: (material anatomical entity) + +AnnotationAssertion( "An anatomical entity that has mass.") +AnnotationAssertion( "CARO:0000006") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "material anatomical entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (immaterial anatomical entity) + +AnnotationAssertion( "Anatomical entity that has no mass.") +AnnotationAssertion( "CARO:0000007") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "immaterial anatomical entity") +EquivalentClasses( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))) +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (multicellular organism) + +AnnotationAssertion( "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell.") +AnnotationAssertion( "CARO:0000012") +AnnotationAssertion(rdfs:comment "MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + +MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.") +AnnotationAssertion(rdfs:label "multicellular organism") +SubClassOf( ) + +# Class: (cell) + +AnnotationAssertion( "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") +AnnotationAssertion( "CL:0000000") +AnnotationAssertion( "GO:0005623") +AnnotationAssertion( "CARO:0000013") +AnnotationAssertion(rdfs:comment "deprecate and replace with CL or GO term?") +AnnotationAssertion(rdfs:label "cell") +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (cell part) + +AnnotationAssertion( "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.") +AnnotationAssertion( "cell component") +AnnotationAssertion( "CARO:0000014") +AnnotationAssertion(rdfs:comment "This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class.") +AnnotationAssertion(rdfs:label "cell part"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (organism subdivision) + +AnnotationAssertion( "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument."@en) +AnnotationAssertion( "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism.") +AnnotationAssertion( "CARO:0000032") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "organism subdivision") +SubClassOf( ) + +# Class: (acellular anatomical structure) + +AnnotationAssertion( "An anatomical structure that has no cells or cell parts as a part.") +AnnotationAssertion( "CARO:0000040") +AnnotationAssertion(rdfs:comment "Example. Insect cuticle, eggshell, hair.") +AnnotationAssertion(rdfs:label "acellular anatomical structure") +EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(0 ) ObjectExactCardinality(0 ))) +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (extraembryonic structure) + +AnnotationAssertion( "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.") +AnnotationAssertion( "CARO:0000042") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: \"Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.\". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids? +") +AnnotationAssertion(rdfs:label "extraembryonic structure") +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (multi-cell-part structure) + +AnnotationAssertion( "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.") +AnnotationAssertion( "multi-cell-component structure") +AnnotationAssertion( "CARO:0001000") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain.") +AnnotationAssertion(rdfs:label "multi-cell-part structure") +SubClassOf( ) +SubClassOf( ObjectIntersectionOf( ObjectAllValuesFrom( ObjectComplementOf()) ObjectMinCardinality(2 ))) +DisjointClasses( ) + +# Class: (gross anatomical part) + +AnnotationAssertion( "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. ") +AnnotationAssertion( ) +AnnotationAssertion( "10.7.2011") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "gross anatomical part"@en) +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organism) + +AnnotationAssertion( "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.") +AnnotationAssertion( "Melissa Haendel") +AnnotationAssertion( "9/18/11") +AnnotationAssertion( "organism or virus or viroid") +AnnotationAssertion(rdfs:label "organism") +SubClassOf( ) + +# Class: (multicellular anatomical structure) + +AnnotationAssertion( "An anatomical structure that has more than one cell as a part.") +AnnotationAssertion( "djs93") +AnnotationAssertion( "Sun Feb 27 10:53:00 GMT 2011") +AnnotationAssertion( "CARO:0010000") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "multicellular anatomical structure") +EquivalentClasses(Annotation(rdfs:comment "There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular organism) + +AnnotationAssertion( "An individual member of a clade of cellular organisms.") +AnnotationAssertion( ) +AnnotationAssertion( "7.16.2011") +AnnotationAssertion( "CARO:0010004") +AnnotationAssertion(rdfs: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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. ") +AnnotationAssertion(rdfs:label "cellular organism") +SubClassOf( ) +SubClassOf( ) + +# Class: (disconnected anatomical group) + +AnnotationAssertion( "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.") +AnnotationAssertion( "CARO:0000054") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "disconnected anatomical group") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectMinCardinality(2 ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular anatomical structure) + +AnnotationAssertion( "An anatomical structure consisting of one or more cells.") +AnnotationAssertion( ) +AnnotationAssertion( "2018-09-28T14:20:19Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "cellular anatomical structure"@en) +EquivalentClasses(Annotation( "With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell") ObjectUnionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (biological entity) + +AnnotationAssertion( "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.") +AnnotationAssertion(rdfs:comment "Important for alignment with Darwin Core class \"Organism\".") +AnnotationAssertion(rdfs:label "biological entity") +SubClassOf( ) + +# Class: (expression pattern) + +AnnotationAssertion( "The mereological sum of all cells in a single organism in which expression of some specified gene occurs.") +AnnotationAssertion(rdfs:label "expression pattern") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anatomical structure) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-9114-8737") Annotation( "https://orcid.org/0000-0002-7073-9172") "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.") +AnnotationAssertion( "CARO:0000003") +AnnotationAssertion( "UBERON:0000061") +AnnotationAssertion( "fly_anatomy.ontology") +AnnotationAssertion( "FBbt:00007001") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anatomical structure") +SubClassOf( ) + +# Class: (material anatomical entity) + +AnnotationAssertion( "CARO:0000006") +AnnotationAssertion( "UBERON:0000465") +AnnotationAssertion( "fly_anatomy.ontology") +AnnotationAssertion( "FBbt:00007016") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "material anatomical entity") +SubClassOf( ) + +# Class: (multicellular structure) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-7073-9172") "Anatomical structure that has multiple cells as parts.") +AnnotationAssertion( ) +AnnotationAssertion( "2010-11-02T02:25:04Z"^^xsd:dateTime) +AnnotationAssertion( "UBERON:0010000") +AnnotationAssertion( "fly_anatomy.ontology") +AnnotationAssertion( "FBbt:00100313") +AnnotationAssertion(rdfs:label "multicellular structure") +SubClassOf( ) + +# Class: (anatomical entity) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-9114-8737") "Anatomical entity which is part_of Drosophila melanogaster.") +AnnotationAssertion( "FBbt_root:00000000") +AnnotationAssertion( "UBERON:0001062") +AnnotationAssertion( "fly_anatomy.ontology") +AnnotationAssertion( "Drosophila") +AnnotationAssertion( "FBbt:10000000") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anatomical entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +DisjointClasses( ) + +# Class: () + +DisjointClasses( ) + +# Class: () -# Class: (molecular_function) - -AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") -AnnotationAssertion( "molecular function") -AnnotationAssertion( "GO:0003674") -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") -AnnotationAssertion(rdfs:label "molecular_function") - -# Class: (biological_process) - -AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-09-19T15:05:24Z") -AnnotationAssertion( "Wikipedia:Biological_process") -AnnotationAssertion( "biological process") -AnnotationAssertion( "physiological process") -AnnotationAssertion( "single organism process") -AnnotationAssertion( "single-organism process") -AnnotationAssertion( "GO:0008150") -AnnotationAssertion(rdfs: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.") -AnnotationAssertion(rdfs:label "biological_process") - -# Class: (kinase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") -AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") -AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") -AnnotationAssertion( "phosphokinase activity") -AnnotationAssertion( "GO:0016301") -AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") -AnnotationAssertion(rdfs:label "kinase activity") -SubClassOf( ) SubClassOf( ObjectHasSelf()) -# Class: (curation status specification) - -AnnotationAssertion( "curation status specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) -AnnotationAssertion( "PERSON:Bill Bug"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion( "OBI_0000266"@en) -AnnotationAssertion(rdfs:label "curation status specification"@en) -EquivalentClasses( ObjectOneOf( )) - -# Class: (quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") -AnnotationAssertion( "PATO:0000001") -AnnotationAssertion(rdfs:label "quality") -SubClassOf( ) - -# Class: (material anatomical entity) - -AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-9114-8737") "Anatomical entity that has mass.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "AAO:0010264") -AnnotationAssertion( "AEO:0000006") -AnnotationAssertion( "BILA:0000006") -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion( "EHDAA2:0003006") -AnnotationAssertion( "FBbt:00007016") -AnnotationAssertion( "FMA:67165") -AnnotationAssertion( "HAO:0000006") -AnnotationAssertion( "TAO:0001836") -AnnotationAssertion( "TGMA:0001826") -AnnotationAssertion( "VHOG:0001721") -AnnotationAssertion( "UBERON:0000465") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "material anatomical entity") -SubClassOf( ) -SubClassOf( ) - -# Class: (anatomical entity) - -AnnotationAssertion(Annotation( "FMA:62955") Annotation( "http://orcid.org/0000-0001-9114-8737") "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "AAO:0010841") -AnnotationAssertion( "AEO:0000000") -AnnotationAssertion( "BILA:0000000") -AnnotationAssertion( "BIRNLEX:6") -AnnotationAssertion( "CARO:0000000") -AnnotationAssertion( "EHDAA2:0002229") -AnnotationAssertion( "FBbt:10000000") -AnnotationAssertion( "FMA:62955") -AnnotationAssertion( "HAO:0000000") -AnnotationAssertion( "MA:0000001") -AnnotationAssertion( "NCIT:C12219") -AnnotationAssertion( "TAO:0100000") -AnnotationAssertion( "TGMA:0001822") -AnnotationAssertion(Annotation( "ncithesaurus:Anatomic_Structure_System_or_Substance") "UMLS:C1515976") -AnnotationAssertion( "WBbt:0000100") -AnnotationAssertion( "XAO:0000000") -AnnotationAssertion( "ZFA:0100000") -AnnotationAssertion( "UBERON:0001062") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anatomical entity") -SubClassOf( ) - - -############################ -# Named Individuals -############################ - -# Individual: (example to be eventually removed) - -AnnotationAssertion( "example to be eventually removed"@en) -AnnotationAssertion(rdfs:label "example to be eventually removed"@en) - -# Individual: (metadata complete) - -AnnotationAssertion( "metadata complete"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "metadata complete"@en) - -# Individual: (organizational term) - -AnnotationAssertion( "organizational term"@en) -AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) -AnnotationAssertion(rdfs:label "organizational term"@en) - -# Individual: (ready for release) - -AnnotationAssertion( "ready for release"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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.\""@en) -AnnotationAssertion(rdfs:label "ready for release"@en) - -# Individual: (metadata incomplete) - -AnnotationAssertion( "metadata incomplete"@en) -AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) -AnnotationAssertion(rdfs:label "metadata incomplete"@en) - -# Individual: (uncurated) - -AnnotationAssertion( "uncurated"@en) -AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) -AnnotationAssertion(rdfs:label "uncurated"@en) - -# Individual: (pending final vetting) - -AnnotationAssertion( "pending final vetting"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "pending final vetting"@en) -ClassAssertion( ) - -# Individual: (to be replaced with external ontology term) - -AnnotationAssertion( "to be replaced with external ontology term"@en) -AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) - -# Individual: (requires discussion) - -AnnotationAssertion( "requires discussion"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "requires discussion"@en) -ClassAssertion( ) +# Class: (planned process) + +AnnotationAssertion( "planned process"@en) +AnnotationAssertion( "planned process") +AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") +AnnotationAssertion( ) +AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) +AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") +AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "branch derived") +AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) +AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "planned process"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (specimen role) + +AnnotationAssertion( "specimen role") +AnnotationAssertion( "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.") +AnnotationAssertion( ) +AnnotationAssertion( "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en) +AnnotationAssertion( "blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen."@en) +AnnotationAssertion( "parasite example +- when parasite in people we study people, people are subjects and parasites are specimen +- when parasite extracted, they become subject in the following study +specimen can later be subject."@en) +AnnotationAssertion( "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.") +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "GROUP: Role Branch") +AnnotationAssertion( "OBI") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "specimen role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) + +# Class: (specimen collection process) + +AnnotationAssertion( "specimen collection process") +AnnotationAssertion( "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective of collecting a specimen.") +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.") +AnnotationAssertion( "Philly2013: The specimen_role for the specimen is created during the specimen collection process.") +AnnotationAssertion( "label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "specimen collection") +AnnotationAssertion( "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession") +AnnotationAssertion( "6/9/09: used at workshop") +AnnotationAssertion(rdfs:label "specimen collection process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (specimen collection objective) + +AnnotationAssertion( "specimen collection objective") +AnnotationAssertion( "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.") +AnnotationAssertion( ) +AnnotationAssertion( "A objective specification to obtain a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:label "specimen collection objective") +SubClassOf( ) + +# Class: (collection of specimens) + +AnnotationAssertion( "collection of specimens"@en) +AnnotationAssertion( "Blood cells collected from multiple donors over the course of a study."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that has two or more specimens as its parts."@en) +AnnotationAssertion( "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/") +AnnotationAssertion( "Person: Chris Stoeckert, Jie Zheng"@en) +AnnotationAssertion( "OBIB, OBI") +AnnotationAssertion( "Biobank") +AnnotationAssertion(rdfs:label "collection of specimens"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) +SubClassOf( ) + +# Class: (specimen) + +AnnotationAssertion( "specimen"@en) +AnnotationAssertion( "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.") +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that has the specimen role."@en) +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "specimen"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) -DifferentIndividuals( ) +DisjointClasses( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -1856,6 +2249,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) diff --git a/imports/obi_import.owl b/imports/obi_import.owl deleted file mode 100644 index f7136c4..0000000 --- a/imports/obi_import.owl +++ /dev/null @@ -1,153 +0,0 @@ -Prefix(:=) -Prefix(owl:=) -Prefix(rdf:=) -Prefix(xml:=) -Prefix(xsd:=) -Prefix(rdfs:=) - - -Ontology( - -Annotation( "en") -Annotation( "Ontology for Biomedical Investigations"@en) -Annotation( "Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester"@en) -Annotation( "Alan Ruttenberg"@en) -Annotation( "Allyson Lister"@en) -Annotation( "Barry Smith"@en) -Annotation( "Bill Bug"@en) -Annotation( "Bjoern Peters"@en) -Annotation( "Carlo Torniai"@en) -Annotation( "Chris Mungall"@en) -Annotation( "Chris Stoeckert"@en) -Annotation( "Chris Taylor"@en) -Annotation( "Christian Bolling"@en) -Annotation( "Cristian Cocos"@en) -Annotation( "Daniel Rubin"@en) -Annotation( "Daniel Schober"@en) -Annotation( "Dawn Field"@en) -Annotation( "Dirk Derom"@en) -Annotation( "Elisabetta Manduchi"@en) -Annotation( "Eric Deutsch"@en) -Annotation( "Frank Gibson"@en) -Annotation( "Gilberto Fragoso"@en) -Annotation( "Helen C. Causton"@en) -Annotation( "Helen Parkinson"@en) -Annotation( "Holger Stenzhorn"@en) -Annotation( "James A. Overton"@en) -Annotation( "James Malone"@en) -Annotation( "Jay Greenbaum"@en) -Annotation( "Jeffrey Grethe"@en) -Annotation( "Jennifer Fostel"@en) -Annotation( "Jessica Turner"@en) -Annotation( "Jie Zheng"@en) -Annotation( "Joe White"@en) -Annotation( "John Westbrook"@en) -Annotation( "Kevin Clancy"@en) -Annotation( "Larisa Soldatova"@en) -Annotation( "Lawrence Hunter"@en) -Annotation( "Liju Fan"@en) -Annotation( "Luisa Montecchi"@en) -Annotation( "Matthew Brush"@en) -Annotation( "Matthew Pocock"@en) -Annotation( "Melanie Courtot"@en) -Annotation( "Melissa Haendel"@en) -Annotation( "Mervi Heiskanen"@en) -Annotation( "Monnie McGee"@en) -Annotation( "Norman Morrison"@en) -Annotation( "Philippe Rocca-Serra"@en) -Annotation( "Phillip Lord"@en) -Annotation( "Pierre Grenon"@en) -Annotation( "Richard Bruskiewich"@en) -Annotation( "Richard Scheuermann"@en) -Annotation( "Robert Stevens"@en) -Annotation( "Ryan R. Brinkman"@en) -Annotation( "Stefan Wiemann"@en) -Annotation( "Susanna-Assunta Sansone"@en) -Annotation( "Tanya Gray"@en) -Annotation( "Tina Hernandez-Boussard"@en) -Annotation( "Trish Whetzel"@en) -Annotation( "Yongqun He"@en) -Annotation( "2009-07-31"^^xsd:date) -Annotation( "An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation."@en) -Annotation( "OWL-DL"@en) -Annotation( ) -Annotation( "An ontology for the annotation of biomedical and functional genomics experiments."@en) -Annotation( "http://creativecommons.org/licenses/by/4.0/") -Annotation( "Ontology for Biomedical Investigations") -Annotation(rdfs:comment "Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.") -Annotation(owl:versionInfo "2023-07-25") -Annotation(owl:versionInfo "2023-08-15") - -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(Datatype(xsd:date)) - -############################ -# Object Properties -############################ - -# Object Property: (has_specified_input) - -AnnotationAssertion( "The inverse property of is_specified_input_of"@en) -AnnotationAssertion(rdfs:label "has_specified_input"@en) -EquivalentObjectProperties( ObjectInverseOf()) -SubObjectPropertyOf( ) - -# Object Property: (is_specified_input_of) - -AnnotationAssertion( "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en) -AnnotationAssertion(rdfs:label "is_specified_input_of"@en) -SubObjectPropertyOf( ) - -# Object Property: (has_specified_output) - -AnnotationAssertion( "The inverse property of is_specified_output_of"@en) -AnnotationAssertion(rdfs:label "has_specified_output"@en) -EquivalentObjectProperties( ObjectInverseOf()) -SubObjectPropertyOf( ) - -# Object Property: (is_specified_output_of) - -AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) -AnnotationAssertion(rdfs:label "is_specified_output_of"@en) -SubObjectPropertyOf( ) - -# Object Property: (achieves_planned_objective) - -AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.") -AnnotationAssertion(rdfs:label "achieves_planned_objective") - -# Object Property: (objective_achieved_by) - -AnnotationAssertion( "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.") -AnnotationAssertion(rdfs:label "objective_achieved_by") - - - -) \ No newline at end of file diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 351c6a4..a683cfb 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for vfbext # Generated using ontology-development-kit -# ODK Version: v1.4.1 +# ODK Version: v1.4.3 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vfbext.Makefile instead @@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.4.1 +ODK_VERSION_MAKEFILE = v1.4.3 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -110,7 +110,7 @@ all_main: $(MAIN_FILES) IMPORTS = ro caro fbbt obi -IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) +IMPORT_ROOTS = $(IMPORTDIR)/merged_import IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) IMPORT_FILES = $(IMPORT_OWL_FILES) @@ -208,7 +208,7 @@ ASSETS = \ $(MAPPING_FILES) RELEASE_ASSETS = \ - $(MAIN_FILES) \ + $(MAIN_FILES) $(IMPORT_FILES) \ $(SUBSET_FILES) .PHONY: all_assets @@ -306,30 +306,28 @@ $(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi +ALL_TERMS_COMBINED = $(patsubst %, $(IMPORTDIR)/%_terms_combined.txt, $(IMPORTS)) +$(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED) + if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi -$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt - if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ - extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \ +$(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \ + extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \ query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi -.PRECIOUS: $(IMPORTDIR)/%_import.owl -## Module for ontology: caro -$(IMPORTDIR)/caro_import.owl: $(MIRRORDIR)/caro.owl - echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in vfbext.Makefile!" && false -## Module for ontology: obi -$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt +$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/%_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ - extract -T $(IMPORTDIR)/obi_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ - remove --base-iri $(URIBASE)/OBI --axioms external --preserve-structure false --trim false \ - query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \ - remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/obi_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi +.PRECIOUS: $(IMPORTDIR)/%_import.owl + .PHONY: refresh-imports refresh-imports: @@ -365,9 +363,8 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports .PHONY: mirror-ro .PRECIOUS: $(MIRRORDIR)/ro.owl mirror-ro: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: caro @@ -375,7 +372,8 @@ mirror-ro: | $(TMPDIR) .PRECIOUS: $(MIRRORDIR)/caro.owl mirror-caro: | $(TMPDIR) if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/caro.owl --create-dirs -o $(MIRRORDIR)/caro.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl &&\ + $(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl && \ + $(ROBOT) remove -i $@.tmp.owl --base-iri http://purl.obolibrary.org/obo/CARO_ --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ mv $@.tmp.owl $(TMPDIR)/$@.owl; fi @@ -383,9 +381,8 @@ mirror-caro: | $(TMPDIR) .PHONY: mirror-fbbt .PRECIOUS: $(MIRRORDIR)/fbbt.owl mirror-fbbt: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/fbbt.owl --create-dirs -o $(MIRRORDIR)/fbbt.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/fbbt.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/fbbt/fbbt-base.owl --create-dirs -o $(MIRRORDIR)/fbbt.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/fbbt.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: obi @@ -393,9 +390,17 @@ mirror-fbbt: | $(TMPDIR) .PRECIOUS: $(MIRRORDIR)/obi.owl mirror-obi: | $(TMPDIR) if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl &&\ + $(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl && \ + $(ROBOT) remove -i $@.tmp.owl --base-iri http://purl.obolibrary.org/obo/OBI_ --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ mv $@.tmp.owl $(TMPDIR)/$@.owl; fi +ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS)) +MERGE_MIRRORS = true + +$(MIRRORDIR)/merged.owl: $(ALL_MIRRORS) + if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(ROBOT) merge $(patsubst %, -i %, $^) -o $@; fi +.PRECIOUS: $(MIRRORDIR)/merged.owl + $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 75d45aa..9f789a8 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -1,9 +1,5 @@ - - - - - + diff --git a/src/ontology/imports/caro_import.owl b/src/ontology/imports/caro_import.owl deleted file mode 100644 index c42ea9b..0000000 --- a/src/ontology/imports/caro_import.owl +++ /dev/null @@ -1,452 +0,0 @@ - - - - - The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. - - Common Anatomy Reference Ontology - - Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendel. - 2023-03-15 - 2023-08-15 - - - - - - - - - - - - - - - - - - - - - - - - - IAO:0000112 - uberon - example_of_usage - true - example_of_usage - example of usage - - - - - - - - definition - - - - - - - - IAO:0000116 - uberon - editor_note - true - editor_note - editor note - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - has_obo_namespace - - - - - - - - - - - - - - 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 - 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. - 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] - - - - - - - - - - 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 - 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]) - 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] - - - - - - - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CARO:0000000 - Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. - anatomical entity - - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - CAROC:Brownsville2014 - - - - - - - - - An anatomical entity that has mass. - CARO:0000006 - - material anatomical entity - - - - - - - - - An anatomical structure consisting of one or more cells. - - 2018-09-28T14:20:19Z - cellular anatomical structure - - - - - - - - - Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. - Important for alignment with Darwin Core class "Organism". - biological entity - - - - - - - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. - expression pattern - - - - - - - diff --git a/src/ontology/imports/fbbt_import.owl b/src/ontology/imports/fbbt_import.owl deleted file mode 100644 index d21cf2e..0000000 --- a/src/ontology/imports/fbbt_import.owl +++ /dev/null @@ -1,2481 +0,0 @@ -Prefix(:=) -Prefix(owl:=) -Prefix(rdf:=) -Prefix(xml:=) -Prefix(xsd:=) 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-Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) 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-Declaration(AnnotationProperty()) -Declaration(AnnotationProperty(rdfs:comment)) -Declaration(AnnotationProperty(rdfs:label)) -Declaration(AnnotationProperty()) -############################ -# Annotation Properties -############################ - -# Annotation Property: (definition) - -AnnotationAssertion(rdfs:label "definition") - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (is a defining property chain axiom) - -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "is a defining property chain axiom") - -# Annotation Property: (is a defining property chain axiom where second argument is reflexive) - -AnnotationAssertion( "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.") -AnnotationAssertion(rdfs:label "is a defining property chain axiom where second argument is reflexive") - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (subset_property) - -AnnotationAssertion(rdfs:label "subset_property") - -# Annotation Property: (database_cross_reference) - -AnnotationAssertion(rdfs:label "database_cross_reference") - -# Annotation Property: (in_subset) - -AnnotationAssertion(rdfs:label "in_subset") - - -############################ -# Object Properties -############################ - -# Object Property: (part_of) - -AnnotationAssertion( "is part of"@en) -AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) -AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) -AnnotationAssertion( "a core relation that holds between a part and its whole"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "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'."@en) -AnnotationAssertion( "part_of"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "BFO:0000050") -AnnotationAssertion( "OBO_REL:part_of") -AnnotationAssertion( "quality") -AnnotationAssertion( "relationship") -AnnotationAssertion( "part_of") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "part_of") -AnnotationAssertion(rdfs:label "part of"@en) -AnnotationAssertion(rdfs:label "part_of") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) -AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (has part) - -AnnotationAssertion( "has part"@en) -AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) -AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) -AnnotationAssertion( "a core relation that holds between a whole and its part"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "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'."@en) -AnnotationAssertion( "has_part"@en) -AnnotationAssertion( ) -AnnotationAssertion( "BFO:0000051") -AnnotationAssertion( "OBO_REL:has_part") -AnnotationAssertion( "quality") -AnnotationAssertion( "relationship") -AnnotationAssertion( "has_part") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "has_part") -AnnotationAssertion(rdfs:label "has part"@en) -AnnotationAssertion(rdfs:label "has_part") -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (preceded by) - -AnnotationAssertion( "preceded by"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "is preceded by"@en) -AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (precedes) - -AnnotationAssertion( "precedes"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "precedes"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (characteristic_of) - -AnnotationAssertion( "inheres in"@en) -AnnotationAssertion( "this fragility is a characteristic of this vase"@en) -AnnotationAssertion( "this red color is a characteristic of this apple"@en) -AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) -AnnotationAssertion( "inheres_in"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0000052") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "characteristic_of") -AnnotationAssertion( "characteristic_of") -AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") -AnnotationAssertion(rdfs:label "characteristic of"@en) -AnnotationAssertion(rdfs:label "characteristic_of") -SubObjectPropertyOf( ) -InverseObjectProperties( ) -FunctionalObjectProperty() - -# Object Property: (has characteristic) - -AnnotationAssertion( "bearer of"@en) -AnnotationAssertion( "this apple is bearer of this red color"@en) -AnnotationAssertion( "this vase is bearer of this fragility"@en) -AnnotationAssertion( "Inverse of characteristic_of"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "bearer_of"@en) -AnnotationAssertion( "is bearer of"@en) -AnnotationAssertion( ) -AnnotationAssertion( "RO:0000053") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "has_characteristic") -AnnotationAssertion( "has_characteristic") -AnnotationAssertion(rdfs:label "has characteristic"@en) -AnnotationAssertion(rdfs:label "has_characteristic") -InverseFunctionalObjectProperty() -ObjectPropertyRange( ) - -# Object Property: (participates in) - -AnnotationAssertion( "participates in"@en) -AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) -AnnotationAssertion( "this input material (or this output material) participates in this process"@en) -AnnotationAssertion( "this investigator participates in this investigation"@en) -AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "participates_in"@en) -AnnotationAssertion(rdfs:label "participates in"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has participant) - -AnnotationAssertion( "has participant"@en) -AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) -AnnotationAssertion( "this investigation has participant this investigator"@en) -AnnotationAssertion( "this process has participant this input material (or this output material)"@en) -AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") -AnnotationAssertion(rdfs:label "has participant"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (function of) - -AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) -AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "function_of"@en) -AnnotationAssertion( "is function of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "function of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (quality of) - -AnnotationAssertion( "this red color is a quality of this apple"@en) -AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) -AnnotationAssertion( "is quality of"@en) -AnnotationAssertion( "quality_of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "quality of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (role of) - -AnnotationAssertion( "this investigator role is a role of this person"@en) -AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "is role of"@en) -AnnotationAssertion( "role_of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "role of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has function) - -AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "has_function"@en) -AnnotationAssertion(rdfs:label "has function"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has quality) - -AnnotationAssertion( "this apple has quality this red color"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "has_quality"@en) -AnnotationAssertion(rdfs:label "has quality"@en) -SubObjectPropertyOf( ) -ObjectPropertyRange( ) - -# Object Property: (has role) - -AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "has_role"@en) -AnnotationAssertion(rdfs:label "has role"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has disposition) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has disposition"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (disposition of) - -AnnotationAssertion( "inverse of has disposition") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "disposition of"@en) -SubObjectPropertyOf( ) - -# Object Property: (has regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has negative regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs: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'.") -AnnotationAssertion(rdfs:label "has negative regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has positive regulatory component activity) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs: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'.") -AnnotationAssertion(rdfs:label "has positive regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has component activity) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") -AnnotationAssertion(rdfs:label "has component activity") -SubObjectPropertyOf( ) - -# Object Property: (has component process) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has component process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulated by) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( ) rdfs: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.") -AnnotationAssertion(rdfs:label "directly regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly negatively regulated by) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly negatively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly positively regulated by) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly positively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has effector activity) - -AnnotationAssertion(Annotation( ) "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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") -AnnotationAssertion(rdfs:label "has effector activity") -SubObjectPropertyOf( ) -FunctionalObjectProperty() - -# Object Property: (ends after) - -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) -AnnotationAssertion(rdfs:label "ends after"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately preceded by) - -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "starts_at_end_of") -AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately precedes) - -AnnotationAssertion( ) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "ends_at_start_of") -AnnotationAssertion( "meets") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately precedes"@en) -SubObjectPropertyOf( ) - -# Object Property: (overlaps) - -AnnotationAssertion( ) -AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") -AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002131") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "overlaps") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "overlaps") -AnnotationAssertion(rdfs:label "overlaps"@en) -AnnotationAssertion(rdfs:label "overlaps") -SubObjectPropertyOf( ) -SymmetricObjectProperty() - -# Object Property: (has component) - -AnnotationAssertion( ) -AnnotationAssertion( "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.") -AnnotationAssertion( "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.") -AnnotationAssertion( "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."@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has component"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (expressed in) - -AnnotationAssertion( "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'") -AnnotationAssertion( ) -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "expressed in"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyDomain( ObjectUnionOf( )) - -# Object Property: (regulates) - -AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "GO") -AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") -AnnotationAssertion( "regulates (processual)") -AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion( "RO:0002211") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulates) - -AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "negatively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002212") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "negatively_regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (positively regulates) - -AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "positively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002213") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "positively_regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (capable_of) - -AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") -AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") -AnnotationAssertion( "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. ") -AnnotationAssertion( ) -AnnotationAssertion( "has function realized in") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "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)\".") -AnnotationAssertion( "RO:0002215") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "capable_of") -AnnotationAssertion( ) -AnnotationAssertion( "capable_of") -AnnotationAssertion(rdfs:label "capable of"@en) -AnnotationAssertion(rdfs:label "capable_of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable_of_part_of) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "has function in") -AnnotationAssertion( "RO:0002216") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "capable_of_part_of") -AnnotationAssertion( "capable_of_part_of") -AnnotationAssertion(rdfs:label "capable of part of"@en) -AnnotationAssertion(rdfs:label "capable_of_part_of") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (temporally related to) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "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.") -AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") -AnnotationAssertion(rdfs:label "temporally related to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has input) - -AnnotationAssertion( ) -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "consumes") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has input"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (acts upstream of) - -AnnotationAssertion( "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.") -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within) - -AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") -AnnotationAssertion( "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.") -AnnotationAssertion( "affects") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (expresses) - -AnnotationAssertion( ) -AnnotationAssertion( "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.") -AnnotationAssertion( ) -AnnotationAssertion( "RO:0002292") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "expresses") -AnnotationAssertion( "expresses") -AnnotationAssertion(rdfs:label "expresses"@en) -AnnotationAssertion(rdfs:label "expresses") -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of, positive effect) - -AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs: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") -AnnotationAssertion(rdfs:label "causally upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of, negative effect) - -AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (characteristic of part of) - -AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") -AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of") -AnnotationAssertion( ) -AnnotationAssertion( "inheres in part of") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "characteristic of part of"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (mereotopologically related to) - -AnnotationAssertion( "A mereological relationship or a topological relationship") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "mereotopologically related to"@en) - -# Object Property: (enables) - -AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") -AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") -AnnotationAssertion( ) -AnnotationAssertion( "catalyzes") -AnnotationAssertion( "executes") -AnnotationAssertion( "has") -AnnotationAssertion( "is catalyzing") -AnnotationAssertion( "is executing") -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enables"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (functionally related to) - -AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") -AnnotationAssertion( ) -AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") -AnnotationAssertion(rdfs:label "functionally related to"@en) - -# Object Property: (part of structure that is capable of) - -AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") -AnnotationAssertion( ) -AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) -SubObjectPropertyOf( ) - -# Object Property: (genomically related to) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "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") -AnnotationAssertion(rdfs:label "genomically related to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (involved in) - -AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") -AnnotationAssertion( ) -AnnotationAssertion( "actively involved in") -AnnotationAssertion( "enables part of") -AnnotationAssertion(rdfs:label "involved in"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enabled by) - -AnnotationAssertion( "inverse of enables") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enabled by"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (regulated by) - -AnnotationAssertion( "inverse of regulates") -AnnotationAssertion( ) -AnnotationAssertion( "regulated by (processual)") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulated by"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulated by) - -AnnotationAssertion( "inverse of negatively regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (positively regulated by) - -AnnotationAssertion( "inverse of positively regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (input of) - -AnnotationAssertion( "inverse of has input") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "input of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally downstream of) - -AnnotationAssertion( ) -AnnotationAssertion( "inverse of upstream of") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately causally downstream of) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (indirectly positively regulates) - -AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly activates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (indirectly negatively regulates) - -AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly inhibits") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (causally related to) - -AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causally related to"@en) - -# Object Property: (causally upstream of) - -AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately causally upstream of) - -AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within) - -AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") -AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") -AnnotationAssertion( ) -AnnotationAssertion( "influences (processual)") -AnnotationAssertion( "affects") -AnnotationAssertion(rdfs:label "causally upstream of or within") -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (causally downstream of or within) - -AnnotationAssertion( "inverse of causally upstream of or within") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally downstream of or within") -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (involved in regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (involved in positive regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in positive regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in negative regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in negative regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in or involved in regulation of) - -AnnotationAssertion( "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") -AnnotationAssertion( "OWL does not allow defining object properties via a Union") -AnnotationAssertion( ) -AnnotationAssertion( "involved in or reguates") -AnnotationAssertion(rdfs:label "involved in or involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (interacts with) - -AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "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.") -AnnotationAssertion( "in pairwise interaction with") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interacts with") -AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) -SymmetricObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (molecularly interacts with) - -AnnotationAssertion( "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.") -AnnotationAssertion( ) -AnnotationAssertion( "binds") -AnnotationAssertion( "molecularly binds with") -AnnotationAssertion(rdfs:label "molecularly interacts with") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) -SubObjectPropertyOf( ) -SymmetricObjectProperty() - -# Object Property: (phosphorylates) - -AnnotationAssertion( "Axiomatization to GO to be added later") -AnnotationAssertion( ) -AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") -AnnotationAssertion(rdfs:label "phosphorylates") -SubObjectPropertyOf( ) - -# Object Property: (directly regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "molecularly controls") -AnnotationAssertion(rdfs:label "directly regulates activity of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly negatively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly inhibits") -AnnotationAssertion( "molecularly decreases activity of") -AnnotationAssertion(rdfs:label "directly negatively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly positively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly activates") -AnnotationAssertion( "molecularly increases activity of") -AnnotationAssertion(rdfs:label "directly positively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (helper property (not for use in curation)) - -AnnotationAssertion( ) -AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") -AnnotationAssertion(rdfs:label "helper property (not for use in curation)") - -# Object Property: (is kinase activity) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "is kinase activity") -SubObjectPropertyOf( ) - -# Object Property: (causal agent in process) - -AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causal agent in process") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (causal relation between processes) - -AnnotationAssertion( "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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causal relation between processes") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (depends on) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "depends on") -AnnotationAssertion(rdfs:seeAlso ) - -# Object Property: (causal relation between entities) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causal relation between entities") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (causally influenced by) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influenced by (entity-centric)") -AnnotationAssertion(rdfs:label "causally influenced by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (interaction relation helper property) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interaction relation helper property") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (molecular interaction relation helper property) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "molecular interaction relation helper property") -SubObjectPropertyOf( ) - -# Object Property: (causally influences) - -AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influences (entity-centric)") -AnnotationAssertion(rdfs:label "causally influences") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulates) - -AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly regulates (processual)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has part structure that is capable of) - -AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has part structure that is capable of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causal relation between material entity and a process) - -AnnotationAssertion( "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.") -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causal relation between material entity and a process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of regulating) - -AnnotationAssertion( "pyrethroid -> growth") -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of negatively regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of negatively regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of positively regulating) - -AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of positively regulating") -SubObjectPropertyOf( ) - -# Object Property: (process has causal agent) - -AnnotationAssertion( "Inverse of 'causal agent in process'") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "process has causal agent") -SubObjectPropertyOf( ) - -# Object Property: (correlated with) - -AnnotationAssertion( "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.") -AnnotationAssertion( "Groups both positive and negative correlation") -AnnotationAssertion(rdfs:label "correlated with") - -# Object Property: (directly positively regulates) - -AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly positively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly positively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (directly negatively regulates) - -AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly negatively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly negatively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enables subfunction) - -AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "enables subfunction") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, positive effect) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, negative effect) - -AnnotationAssertion( "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") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (regulates activity of) - -AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (indirectly causally upstream of) - -AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) -SubObjectPropertyOf( ) - -# Object Property: (indirectly regulates) - -AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (device utilizes material) - -AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") -AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") -AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( "2021-11-08T12:00:00Z") -AnnotationAssertion( "utilizes") -AnnotationAssertion(rdfs:label "device utilizes material"@en) - -# Object Property: (positively correlated with) - -AnnotationAssertion( "A relation between entities in which one increases or decreases as the other does the same."@en) -AnnotationAssertion( "directly correlated with"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively correlated with"@en) -SubObjectPropertyOf( ) -SymmetricObjectProperty() -ReflexiveObjectProperty() - -# Object Property: (regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates characteristic") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (positively regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulates characteristic") -SubObjectPropertyOf( ) - -# Object Property: (negatively regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulates characteristic") -SubObjectPropertyOf( ) - - - -############################ -# Classes -############################ - -# Class: (continuant) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (occurrent) - -AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) -AnnotationAssertion(rdfs:label "occurrent"@en) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (independent continuant) - -AnnotationAssertion( "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])"@en) -AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) -AnnotationAssertion(rdfs:label "independent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (process) - -AnnotationAssertion( "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])"@en) -AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) -AnnotationAssertion(rdfs:label "process"@en) -SubClassOf( ) - -# Class: (disposition) - -AnnotationAssertion(rdfs:label "disposition"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (realizable entity) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "realizable entity"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (quality) - -AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (specifically dependent continuant) - -AnnotationAssertion( "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])"@en) -AnnotationAssertion(rdfs:comment "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."@en) -AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (role) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "role"@en) -SubClassOf( ) - -# Class: (generically dependent continuant) - -AnnotationAssertion( "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])"@en) -AnnotationAssertion(rdfs:comment "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."@en) -AnnotationAssertion(rdfs:label "generically dependent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (function) - -AnnotationAssertion(rdfs:label "function"@en) -SubClassOf( ) - -# Class: (material entity) - -AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) -AnnotationAssertion(rdfs:label "material entity"@en) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (immaterial entity) - -AnnotationAssertion(rdfs:label "immaterial entity"@en) -SubClassOf( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (anatomical entity) - -AnnotationAssertion(Annotation( "CAROC:Brownsville2014") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") -AnnotationAssertion( "CARO:0000000") -AnnotationAssertion(rdfs:comment "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.") -AnnotationAssertion(rdfs:label "anatomical entity") -SubClassOf( ) -DisjointUnion( ) - -# Class: (material anatomical entity) - -AnnotationAssertion( "An anatomical entity that has mass.") -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "material anatomical entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (immaterial anatomical entity) - -AnnotationAssertion( "Anatomical entity that has no mass.") -AnnotationAssertion( "CARO:0000007") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immaterial anatomical entity") -EquivalentClasses( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))) -SubClassOf( ) -SubClassOf( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (biological entity) - -AnnotationAssertion( "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.") -AnnotationAssertion(rdfs:comment "Important for alignment with Darwin Core class \"Organism\".") -AnnotationAssertion(rdfs:label "biological entity") -SubClassOf( ) - -# Class: (anatomical structure) - -AnnotationAssertion(Annotation( "CARO:MAH") Annotation( "FBC:DOS") "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.") -AnnotationAssertion( "CARO:0000003") -AnnotationAssertion( "UBERON:0000061") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "FBbt:00007001") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anatomical structure") -SubClassOf( ) - -# Class: (material anatomical entity) - -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion( "UBERON:0000465") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "FBbt:00007016") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "material anatomical entity") -SubClassOf( ) - -# Class: (multicellular structure) - -AnnotationAssertion(Annotation( "FBC:DOS") "Anatomical structure that has multiple cells as parts.") -AnnotationAssertion( ) -AnnotationAssertion( "2010-11-02T02:25:04Z"^^xsd:dateTime) -AnnotationAssertion( "UBERON:0010000") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "FBbt:00100313") -AnnotationAssertion(rdfs:label "multicellular structure") -SubClassOf( ) - -# Class: (anatomical entity) - -AnnotationAssertion(Annotation( "CARO:MAH") "Anatomical entity which is part_of Drosophila melanogaster.") -AnnotationAssertion( "FBbt_root:00000000") -AnnotationAssertion( "UBERON:0001062") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "Drosophila") -AnnotationAssertion( "FBbt:10000000") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anatomical entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -DisjointClasses( ) - -# Class: (molecular_function) - -AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") -AnnotationAssertion( "GO:0005554") -AnnotationAssertion( "molecular function") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0003674") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") -AnnotationAssertion(rdfs:label "molecular_function") - -# Class: (catalytic activity) - -AnnotationAssertion(Annotation( "GOC:vw") Annotation( "ISBN:0198506732") "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.") -AnnotationAssertion( "Wikipedia:Enzyme") -AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "enzyme activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0003824") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "catalytic activity") -SubClassOf( ) - -# Class: (biological_process) - -AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.") -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24968"^^xsd:anyURI) -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-09-19T15:05:24Z") -AnnotationAssertion( "GO:0000004") -AnnotationAssertion( "GO:0007582") -AnnotationAssertion( "GO:0044699") -AnnotationAssertion( "Wikipedia:Biological_process") -AnnotationAssertion( "biological process") -AnnotationAssertion( "physiological process") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "single organism process") -AnnotationAssertion( "single-organism process") -AnnotationAssertion( "GO:0008150") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs: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.") -AnnotationAssertion(rdfs:label "biological_process") - -# Class: (kinase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") -AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") -AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") -AnnotationAssertion( "phosphokinase activity") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016301") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") -AnnotationAssertion(rdfs:label "kinase activity") -SubClassOf( ) -SubClassOf( ObjectHasSelf()) - -# Class: (transferase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.") -AnnotationAssertion( "EC:2.-.-.-") -AnnotationAssertion(Annotation(rdfs:label "PE is converted to PS by PTDSS2") "Reactome:R-HSA-1483089") -AnnotationAssertion(Annotation(rdfs:label "PC is converted to PS by PTDSS1") "Reactome:R-HSA-1483186") -AnnotationAssertion(Annotation(rdfs:label "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK") "Reactome:R-HSA-5668414") -AnnotationAssertion(Annotation(rdfs:label "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248") "Reactome:R-HSA-8868783") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016740") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "transferase activity") -SubClassOf( ) - -# Class: (transferase activity, transferring phosphorus-containing groups) - -AnnotationAssertion(Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") -AnnotationAssertion( "EC:2.7.-.-") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0016772") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.") -AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups") -SubClassOf( ) - -# Class: (root) - -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "all") -AnnotationAssertion( "NCBITaxon:1") -AnnotationAssertion(rdfs:label "root") - -# Class: (Ecdysozoa) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:1206794") -AnnotationAssertion(rdfs:label "Ecdysozoa") -SubClassOf( ) - -# Class: (cellular organisms) - -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "biota") -AnnotationAssertion( "NCBITaxon:131567") -AnnotationAssertion(rdfs:label "cellular organisms") -SubClassOf( ) - -# Class: (Pancrustacea) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "PMID:10874751") -AnnotationAssertion( "PMID:11557979") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:197562") -AnnotationAssertion(rdfs:label "Pancrustacea") -SubClassOf( ) - -# Class: (Mandibulata) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "PMID:11557979") -AnnotationAssertion( "PMID:9727836") -AnnotationAssertion(Annotation( ) "mandibulates") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:197563") -AnnotationAssertion(rdfs:label "Mandibulata") -SubClassOf( ) - -# Class: (Eukaryota) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "PMID:23020233") -AnnotationAssertion( "PMID:30257078") -AnnotationAssertion(Annotation( ) "eucaryotes") -AnnotationAssertion(Annotation( ) "eukaryotes") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Eucarya") -AnnotationAssertion(Annotation( ) "Eucaryotae") -AnnotationAssertion(Annotation( ) "Eukarya") -AnnotationAssertion(Annotation( ) "Eukaryotae") -AnnotationAssertion(Annotation( ) "eukaryotes") -AnnotationAssertion( "NCBITaxon:2759") -AnnotationAssertion(rdfs:label "Eukaryota") -SubClassOf( ) - -# Class: (Sophophora) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:32341") -AnnotationAssertion(rdfs:label "Sophophora") -SubClassOf( ) - -# Class: (melanogaster group) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:32346") -AnnotationAssertion(rdfs:label "melanogaster group") -SubClassOf( ) - -# Class: (melanogaster subgroup) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:32351") -AnnotationAssertion(rdfs:label "melanogaster subgroup") -SubClassOf( ) - -# Class: (Opisthokonta) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Fungi/Metazoa group") -AnnotationAssertion(Annotation( ) "opisthokonts") -AnnotationAssertion( "NCBITaxon:33154") -AnnotationAssertion(rdfs:label "Opisthokonta") -SubClassOf( ) - -# Class: (Metazoa) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "metazoans") -AnnotationAssertion(Annotation( ) "multicellular animals") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Animalia") -AnnotationAssertion(Annotation( ) "animals") -AnnotationAssertion( "NCBITaxon:33208") -AnnotationAssertion(rdfs:label "Metazoa") -SubClassOf( ) - -# Class: (Bilateria) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:33213") -AnnotationAssertion(rdfs:label "Bilateria") -SubClassOf( ) - -# Class: (Protostomia) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:33317") -AnnotationAssertion(rdfs:label "Protostomia") -SubClassOf( ) - -# Class: (Neoptera) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:33340") -AnnotationAssertion(rdfs:label "Neoptera") -SubClassOf( ) - -# Class: (Endopterygota) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Holometabola") -AnnotationAssertion( "NCBITaxon:33392") -AnnotationAssertion(rdfs:label "Endopterygota") -SubClassOf( ) - -# Class: (Muscomorpha) - -AnnotationAssertion( ) -AnnotationAssertion( "NCBITaxon:43732") -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Asilomorpha") -AnnotationAssertion( "NCBITaxon:43733") -AnnotationAssertion(rdfs:label "Muscomorpha") -SubClassOf( ) - -# Class: (Schizophora) - -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:43738") -AnnotationAssertion(rdfs:label "Schizophora") -SubClassOf( ) - -# Class: (Acalyptratae) - -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:43741") -AnnotationAssertion(rdfs:label "Acalyptratae") -SubClassOf( ) - -# Class: (Ephydroidea) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:43746") -AnnotationAssertion(rdfs:label "Ephydroidea") -SubClassOf( ) - -# Class: (Drosophilinae) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:43845") -AnnotationAssertion(rdfs:label "Drosophilinae") -SubClassOf( ) - -# Class: (Drosophilini) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:46877") -AnnotationAssertion(rdfs:label "Drosophilini") -SubClassOf( ) - -# Class: (Cyclorrhapha) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:480117") -AnnotationAssertion(rdfs:label "Cyclorrhapha") -SubClassOf( ) - -# Class: (Eremoneura) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:480118") -AnnotationAssertion(rdfs:label "Eremoneura") -SubClassOf( ) - -# Class: (Insecta) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "true insects") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "insects") -AnnotationAssertion( "NCBITaxon:50557") -AnnotationAssertion(rdfs:label "Insecta") -SubClassOf( ) - -# Class: (Eumetazoa) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:6072") -AnnotationAssertion(rdfs:label "Eumetazoa") -SubClassOf( ) - -# Class: (Arthropoda) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "arthropods") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "arthropods") -AnnotationAssertion( "NCBITaxon:6656") -AnnotationAssertion(rdfs:label "Arthropoda") -SubClassOf( ) - -# Class: (Hexapoda) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "insects") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Atelocerata") -AnnotationAssertion(Annotation( ) "Tracheata") -AnnotationAssertion(Annotation( ) "Uniramia") -AnnotationAssertion(Annotation( ) "hexapods") -AnnotationAssertion( "NCBITaxon:6960") -AnnotationAssertion(rdfs:label "Hexapoda") -SubClassOf( ) - -# Class: (Diptera) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "flies") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "flies") -AnnotationAssertion( "NCBITaxon:7147") -AnnotationAssertion(rdfs:label "Diptera") -SubClassOf( ) - -# Class: (Brachycera) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:7203") -AnnotationAssertion(rdfs:label "Brachycera") -SubClassOf( ) - -# Class: (Drosophilidae) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "pomace flies") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:7214") -AnnotationAssertion(rdfs:label "Drosophilidae") -SubClassOf( ) - -# Class: (Drosophila ) - -AnnotationAssertion( ) -AnnotationAssertion( "NCBITaxon:7326") -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "Drosophila") -AnnotationAssertion(Annotation( ) "fruit flies") -AnnotationAssertion(Annotation( ) "fruit fly") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:7215") -AnnotationAssertion(rdfs:label "Drosophila ") -SubClassOf( ) - -# Class: (Drosophila melanogaster) - -AnnotationAssertion( ) -AnnotationAssertion( "NCBITaxon:2267365") -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "fruit fly") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion(Annotation( ) "Sophophora melanogaster") -AnnotationAssertion( "NCBITaxon:7227") -AnnotationAssertion(rdfs:label "Drosophila melanogaster") -SubClassOf( ) - -# Class: (Pterygota ) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion(Annotation( ) "Pterygota") -AnnotationAssertion(Annotation( ) "winged insects") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:7496") -AnnotationAssertion(rdfs:label "Pterygota ") -SubClassOf( ) - -# Class: (Dicondylia) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:85512") -AnnotationAssertion(rdfs:label "Dicondylia") -SubClassOf( ) - -# Class: (Panarthropoda) - -AnnotationAssertion( ) -AnnotationAssertion( "GC_ID:1") -AnnotationAssertion( "ncbi_taxonomy") -AnnotationAssertion( "NCBITaxon:88770") -AnnotationAssertion(rdfs:label "Panarthropoda") -SubClassOf( ) - -# Class: (quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") -AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.") -AnnotationAssertion( "PATO:0000072") -AnnotationAssertion( "trait") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0000001") -AnnotationAssertion(rdfs:label "quality") - -# Class: (mass) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0000125") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism.") -AnnotationAssertion(rdfs:label "mass") -SubClassOf( ) - -# Class: (physical quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.") -AnnotationAssertion( "PATO:0002079") -AnnotationAssertion( "Wikipedia:Physical_property") -AnnotationAssertion( "relational physical quality") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0001018") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "physical quality") -SubClassOf( ) - -# Class: (physical object quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A quality which inheres in a continuant.") -AnnotationAssertion( "PATO:0001237") -AnnotationAssertion( "PATO:0001238") -AnnotationAssertion( "snap:Quality") -AnnotationAssertion( "monadic quality of a continuant") -AnnotationAssertion( "multiply inhering quality of a physical entity") -AnnotationAssertion( "multiply inhering quality of a physical entity ") -AnnotationAssertion( "quality of a continuant") -AnnotationAssertion( "quality of a single physical entity") -AnnotationAssertion( "quality of an object") -AnnotationAssertion( "quality of continuant") -AnnotationAssertion( "monadic quality of an object") -AnnotationAssertion( "monadic quality of continuant") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0001241") -AnnotationAssertion(rdfs: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.") -AnnotationAssertion(rdfs:label "physical object quality") -SubClassOf( ) - - -EquivalentClasses(Annotation(rdfs:comment "Should belong in BFO, but lives in caro for now.") ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) -SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(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") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "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'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(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'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(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()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -) \ No newline at end of file diff --git a/imports/ro_import.owl b/src/ontology/imports/merged_import.owl similarity index 73% rename from imports/ro_import.owl rename to src/ontology/imports/merged_import.owl index ca7276c..c2ad10e 100644 --- a/imports/ro_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,9 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-08-15") +Ontology( + +Annotation(owl:versionInfo "2023-10-26") Declaration(Class()) Declaration(Class()) @@ -23,22 +22,68 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -125,9 +170,9 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -135,24 +180,16 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -162,11 +199,13 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -179,19 +218,19 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -200,50 +239,24 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(Datatype(xsd:date)) ############################ # Annotation Properties ############################ # Annotation Property: (definition) -AnnotationAssertion( "definition"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) -AnnotationAssertion( "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. "@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") # Annotation Property: () @@ -276,17 +289,29 @@ SubAnnotationPropertyOf( < SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: () -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () -# Annotation Property: () +SubAnnotationPropertyOf( ) -SubAnnotationPropertyOf( ) +# Annotation Property: () -# Annotation Property: () +SubAnnotationPropertyOf( ) -SubAnnotationPropertyOf( ) +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) # Annotation Property: (subset_property) @@ -360,6 +385,35 @@ AnnotationAssertion(rdfs:label "has SubObjectPropertyOf( ) TransitiveObjectProperty() +# Object Property: (realized in) + +AnnotationAssertion( "realized in"@en) +AnnotationAssertion( "this disease is realized in this disease course"@en) +AnnotationAssertion( "this fragility is realized in this shattering"@en) +AnnotationAssertion( "this investigator role is realized in this investigation"@en) +AnnotationAssertion( "is realized by"@en) +AnnotationAssertion( "realized_in"@en) +AnnotationAssertion( "[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])"@en) +AnnotationAssertion(rdfs:comment "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") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realized in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (realizes) + +AnnotationAssertion( "realizes"@en) +AnnotationAssertion( "this disease course realizes this disease"@en) +AnnotationAssertion( "this investigation realizes this investigator role"@en) +AnnotationAssertion( "this shattering realizes this fragility"@en) +AnnotationAssertion( "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])"@en) +AnnotationAssertion(rdfs:comment "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") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (preceded by) AnnotationAssertion( "preceded by"@en) @@ -367,7 +421,7 @@ AnnotationAssertion( "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."@en) AnnotationAssertion( "is preceded by"@en) AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "preceded by"@en) SubObjectPropertyOf( ) @@ -387,6 +441,72 @@ TransitiveObjectProperty() ObjectPropertyDomain( ) ObjectPropertyRange( ) +# Object Property: (has_specified_input) + +AnnotationAssertion( "has_specified_input"@en) +AnnotationAssertion( "has_specified_input") +AnnotationAssertion( "see is_input_of example_of_usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_input_of"@en) +AnnotationAssertion( "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Coutot") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has_specified_input"@en) +EquivalentObjectProperties( ObjectInverseOf()) +SubObjectPropertyOf( ) + +# Object Property: (is_specified_input_of) + +AnnotationAssertion( "is_specified_input_of") +AnnotationAssertion( "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "is_specified_input_of"@en) +SubObjectPropertyOf( ) + +# Object Property: (has_specified_output) + +AnnotationAssertion( "has_specified_output"@en) +AnnotationAssertion( "has_specified_output") +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_output_of"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has_specified_output"@en) +EquivalentObjectProperties( ObjectInverseOf()) +SubObjectPropertyOf( ) + +# Object Property: (is_specified_output_of) + +AnnotationAssertion( "is_specified_output_of"@en) +AnnotationAssertion( "is_specified_output_of") +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "is_specified_output_of"@en) +SubObjectPropertyOf( ) + +# Object Property: (achieves_planned_objective) + +AnnotationAssertion( "achieves_planned_objective") +AnnotationAssertion( "A cell sorting process achieves the objective specification 'material separation objective'") +AnnotationAssertion( ) +AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.") +AnnotationAssertion( "BP, AR, PPPB branch") +AnnotationAssertion( "PPPB branch derived") +AnnotationAssertion( "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch") +AnnotationAssertion(rdfs:label "achieves_planned_objective") + # Object Property: (characteristic of) AnnotationAssertion( "inheres in"@en) @@ -437,11 +557,30 @@ AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion( "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."@en) AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) +# Object Property: (is concretized as) + +AnnotationAssertion( "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)."@en) +AnnotationAssertion( "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)."@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion(rdfs:label "is concretized as"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (concretizes) + +AnnotationAssertion( "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)."@en) +AnnotationAssertion( "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)."@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion(rdfs:label "concretizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (function of) AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) @@ -1362,12 +1501,6 @@ AnnotationAssertion( "process has causal agent") SubObjectPropertyOf( ) -# Object Property: (correlated with) - -AnnotationAssertion( "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.") -AnnotationAssertion( "Groups both positive and negative correlation") -AnnotationAssertion(rdfs:label "correlated with") - # Object Property: (directly positively regulates) AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") @@ -1396,6 +1529,16 @@ AnnotationAssertion(rdfs:seeAlso "ht SubObjectPropertyOf( ) SubObjectPropertyOf( ) +# Object Property: (realized in response to stimulus) + +AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-12-26T19:45:49Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "realized in response to stimulus") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (enables subfunction) AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") @@ -1466,6 +1609,49 @@ AnnotationAssertion(rdfs:label "caus AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) +# Object Property: (realized in response to) + +AnnotationAssertion( "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.") +AnnotationAssertion( "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") +AnnotationAssertion( "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.") +AnnotationAssertion( "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.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "triggered by process") +AnnotationAssertion(rdfs:label "realized in response to"@en) +AnnotationAssertion(rdfs:seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (generically depends on) + +AnnotationAssertion( "Genetic information generically depend on molecules of DNA.") +AnnotationAssertion( "The novel *War and Peace* generically depends on this copy of the novel.") +AnnotationAssertion( "The pattern shared by chess boards generically depends on any chess board.") +AnnotationAssertion( "The score of a symphony g-depends on a copy of the score.") +AnnotationAssertion( "This pdf file generically depends on this server.") +AnnotationAssertion( "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion( "g-depends on") +AnnotationAssertion(rdfs:label "generically depends on") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is carrier of) + +AnnotationAssertion( "Molecules of DNA are carriers of genetic information.") +AnnotationAssertion( "This copy of *War and Peace* is carrier of the novel written by Tolstoy.") +AnnotationAssertion( "This hard drive is carrier of these data items.") +AnnotationAssertion( "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion(rdfs:label "is carrier of"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (regulates activity of) AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") @@ -1500,20 +1686,10 @@ AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( "2021-11-08T12:00:00Z") +AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) -# Object Property: (positively correlated with) - -AnnotationAssertion( "A relation between entities in which one increases or decreases as the other does the same."@en) -AnnotationAssertion( "directly correlated with"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively correlated with"@en) -SubObjectPropertyOf( ) -SymmetricObjectProperty() -ReflexiveObjectProperty() - # Object Property: (regulates characteristic) AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") @@ -1628,190 +1804,407 @@ SubClassOf( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) AnnotationAssertion(rdfs:label "material entity"@en) SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (immaterial entity) + +AnnotationAssertion(rdfs:label "immaterial entity"@en) +SubClassOf( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (anatomical entity) + +AnnotationAssertion(Annotation( "CAROC:Brownsville2014") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion( "CARO:0000000") +AnnotationAssertion(rdfs:comment "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.") +AnnotationAssertion(rdfs:label "anatomical entity") +SubClassOf( ) + +# Class: (connected anatomical structure) + +AnnotationAssertion( "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.") +AnnotationAssertion( "CARO:0000003") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.") +AnnotationAssertion(rdfs:label "connected anatomical structure") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organism substance) + +AnnotationAssertion( "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle.") +AnnotationAssertion( "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome.") +AnnotationAssertion( "portion of organism substance") +AnnotationAssertion( "CARO:0000004") +AnnotationAssertion(rdfs:comment "Note - CARO explicitly declares organisms substances to be part of (some) organism.") +AnnotationAssertion(rdfs:label "organism substance") +SubClassOf( ) + +# Class: (material anatomical entity) + +AnnotationAssertion( "An anatomical entity that has mass.") +AnnotationAssertion( "CARO:0000006") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "material anatomical entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (immaterial anatomical entity) + +AnnotationAssertion( "Anatomical entity that has no mass.") +AnnotationAssertion( "CARO:0000007") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "immaterial anatomical entity") +EquivalentClasses( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))) +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (multicellular organism) + +AnnotationAssertion( "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell.") +AnnotationAssertion( "CARO:0000012") +AnnotationAssertion(rdfs:comment "MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + +MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.") +AnnotationAssertion(rdfs:label "multicellular organism") +SubClassOf( ) + +# Class: (cell) + +AnnotationAssertion( "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") +AnnotationAssertion( "CL:0000000") +AnnotationAssertion( "GO:0005623") +AnnotationAssertion( "CARO:0000013") +AnnotationAssertion(rdfs:comment "deprecate and replace with CL or GO term?") +AnnotationAssertion(rdfs:label "cell") +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (cell part) + +AnnotationAssertion( "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.") +AnnotationAssertion( "cell component") +AnnotationAssertion( "CARO:0000014") +AnnotationAssertion(rdfs:comment "This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class.") +AnnotationAssertion(rdfs:label "cell part"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (organism subdivision) + +AnnotationAssertion( "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument."@en) +AnnotationAssertion( "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism.") +AnnotationAssertion( "CARO:0000032") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "organism subdivision") +SubClassOf( ) + +# Class: (acellular anatomical structure) + +AnnotationAssertion( "An anatomical structure that has no cells or cell parts as a part.") +AnnotationAssertion( "CARO:0000040") +AnnotationAssertion(rdfs:comment "Example. Insect cuticle, eggshell, hair.") +AnnotationAssertion(rdfs:label "acellular anatomical structure") +EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(0 ) ObjectExactCardinality(0 ))) +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (extraembryonic structure) + +AnnotationAssertion( "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.") +AnnotationAssertion( "CARO:0000042") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: \"Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.\". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids? +") +AnnotationAssertion(rdfs:label "extraembryonic structure") +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (multi-cell-part structure) + +AnnotationAssertion( "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.") +AnnotationAssertion( "multi-cell-component structure") +AnnotationAssertion( "CARO:0001000") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain.") +AnnotationAssertion(rdfs:label "multi-cell-part structure") +SubClassOf( ) +SubClassOf( ObjectIntersectionOf( ObjectAllValuesFrom( ObjectComplementOf()) ObjectMinCardinality(2 ))) +DisjointClasses( ) + +# Class: (gross anatomical part) + +AnnotationAssertion( "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. ") +AnnotationAssertion( ) +AnnotationAssertion( "10.7.2011") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "gross anatomical part"@en) +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organism) + +AnnotationAssertion( "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.") +AnnotationAssertion( "Melissa Haendel") +AnnotationAssertion( "9/18/11") +AnnotationAssertion( "organism or virus or viroid") +AnnotationAssertion(rdfs:label "organism") +SubClassOf( ) + +# Class: (multicellular anatomical structure) + +AnnotationAssertion( "An anatomical structure that has more than one cell as a part.") +AnnotationAssertion( "djs93") +AnnotationAssertion( "Sun Feb 27 10:53:00 GMT 2011") +AnnotationAssertion( "CARO:0010000") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "multicellular anatomical structure") +EquivalentClasses(Annotation(rdfs:comment "There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular organism) + +AnnotationAssertion( "An individual member of a clade of cellular organisms.") +AnnotationAssertion( ) +AnnotationAssertion( "7.16.2011") +AnnotationAssertion( "CARO:0010004") +AnnotationAssertion(rdfs: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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. ") +AnnotationAssertion(rdfs:label "cellular organism") +SubClassOf( ) +SubClassOf( ) + +# Class: (disconnected anatomical group) + +AnnotationAssertion( "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.") +AnnotationAssertion( "CARO:0000054") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "disconnected anatomical group") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectMinCardinality(2 ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular anatomical structure) + +AnnotationAssertion( "An anatomical structure consisting of one or more cells.") +AnnotationAssertion( ) +AnnotationAssertion( "2018-09-28T14:20:19Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "cellular anatomical structure"@en) +EquivalentClasses(Annotation( "With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell") ObjectUnionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (biological entity) + +AnnotationAssertion( "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.") +AnnotationAssertion(rdfs:comment "Important for alignment with Darwin Core class \"Organism\".") +AnnotationAssertion(rdfs:label "biological entity") +SubClassOf( ) + +# Class: (expression pattern) + +AnnotationAssertion( "The mereological sum of all cells in a single organism in which expression of some specified gene occurs.") +AnnotationAssertion(rdfs:label "expression pattern") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (anatomical structure) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-9114-8737") Annotation( "https://orcid.org/0000-0002-7073-9172") "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.") +AnnotationAssertion( "CARO:0000003") +AnnotationAssertion( "UBERON:0000061") +AnnotationAssertion( "fly_anatomy.ontology") +AnnotationAssertion( "FBbt:00007001") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anatomical structure") +SubClassOf( ) + +# Class: (material anatomical entity) + +AnnotationAssertion( "CARO:0000006") +AnnotationAssertion( "UBERON:0000465") +AnnotationAssertion( "fly_anatomy.ontology") +AnnotationAssertion( "FBbt:00007016") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "material anatomical entity") +SubClassOf( ) + +# Class: (multicellular structure) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0002-7073-9172") "Anatomical structure that has multiple cells as parts.") +AnnotationAssertion( ) +AnnotationAssertion( "2010-11-02T02:25:04Z"^^xsd:dateTime) +AnnotationAssertion( "UBERON:0010000") +AnnotationAssertion( "fly_anatomy.ontology") +AnnotationAssertion( "FBbt:00100313") +AnnotationAssertion(rdfs:label "multicellular structure") +SubClassOf( ) + +# Class: (anatomical entity) + +AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-9114-8737") "Anatomical entity which is part_of Drosophila melanogaster.") +AnnotationAssertion( "FBbt_root:00000000") +AnnotationAssertion( "UBERON:0001062") +AnnotationAssertion( "fly_anatomy.ontology") +AnnotationAssertion( "Drosophila") +AnnotationAssertion( "FBbt:10000000") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anatomical entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +DisjointClasses( ) + +# Class: () + +DisjointClasses( ) + +# Class: () -# Class: (molecular_function) - -AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") -AnnotationAssertion( "molecular function") -AnnotationAssertion( "GO:0003674") -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") -AnnotationAssertion(rdfs:label "molecular_function") - -# Class: (biological_process) - -AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-09-19T15:05:24Z") -AnnotationAssertion( "Wikipedia:Biological_process") -AnnotationAssertion( "biological process") -AnnotationAssertion( "physiological process") -AnnotationAssertion( "single organism process") -AnnotationAssertion( "single-organism process") -AnnotationAssertion( "GO:0008150") -AnnotationAssertion(rdfs: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.") -AnnotationAssertion(rdfs:label "biological_process") - -# Class: (kinase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") -AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") -AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") -AnnotationAssertion( "phosphokinase activity") -AnnotationAssertion( "GO:0016301") -AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") -AnnotationAssertion(rdfs:label "kinase activity") -SubClassOf( ) SubClassOf( ObjectHasSelf()) -# Class: (curation status specification) - -AnnotationAssertion( "curation status specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) -AnnotationAssertion( "PERSON:Bill Bug"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion( "OBI_0000266"@en) -AnnotationAssertion(rdfs:label "curation status specification"@en) -EquivalentClasses( ObjectOneOf( )) - -# Class: (quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") -AnnotationAssertion( "PATO:0000001") -AnnotationAssertion(rdfs:label "quality") -SubClassOf( ) - -# Class: (material anatomical entity) - -AnnotationAssertion(Annotation( "http://orcid.org/0000-0001-9114-8737") "Anatomical entity that has mass.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "AAO:0010264") -AnnotationAssertion( "AEO:0000006") -AnnotationAssertion( "BILA:0000006") -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion( "EHDAA2:0003006") -AnnotationAssertion( "FBbt:00007016") -AnnotationAssertion( "FMA:67165") -AnnotationAssertion( "HAO:0000006") -AnnotationAssertion( "TAO:0001836") -AnnotationAssertion( "TGMA:0001826") -AnnotationAssertion( "VHOG:0001721") -AnnotationAssertion( "UBERON:0000465") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "material anatomical entity") -SubClassOf( ) -SubClassOf( ) - -# Class: (anatomical entity) - -AnnotationAssertion(Annotation( "FMA:62955") Annotation( "http://orcid.org/0000-0001-9114-8737") "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.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "AAO:0010841") -AnnotationAssertion( "AEO:0000000") -AnnotationAssertion( "BILA:0000000") -AnnotationAssertion( "BIRNLEX:6") -AnnotationAssertion( "CARO:0000000") -AnnotationAssertion( "EHDAA2:0002229") -AnnotationAssertion( "FBbt:10000000") -AnnotationAssertion( "FMA:62955") -AnnotationAssertion( "HAO:0000000") -AnnotationAssertion( "MA:0000001") -AnnotationAssertion( "NCIT:C12219") -AnnotationAssertion( "TAO:0100000") -AnnotationAssertion( "TGMA:0001822") -AnnotationAssertion(Annotation( "ncithesaurus:Anatomic_Structure_System_or_Substance") "UMLS:C1515976") -AnnotationAssertion( "WBbt:0000100") -AnnotationAssertion( "XAO:0000000") -AnnotationAssertion( "ZFA:0100000") -AnnotationAssertion( "UBERON:0001062") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "anatomical entity") -SubClassOf( ) - - -############################ -# Named Individuals -############################ - -# Individual: (example to be eventually removed) - -AnnotationAssertion( "example to be eventually removed"@en) -AnnotationAssertion(rdfs:label "example to be eventually removed"@en) - -# Individual: (metadata complete) - -AnnotationAssertion( "metadata complete"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "metadata complete"@en) - -# Individual: (organizational term) - -AnnotationAssertion( "organizational term"@en) -AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) -AnnotationAssertion(rdfs:label "organizational term"@en) - -# Individual: (ready for release) - -AnnotationAssertion( "ready for release"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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.\""@en) -AnnotationAssertion(rdfs:label "ready for release"@en) - -# Individual: (metadata incomplete) - -AnnotationAssertion( "metadata incomplete"@en) -AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) -AnnotationAssertion(rdfs:label "metadata incomplete"@en) - -# Individual: (uncurated) - -AnnotationAssertion( "uncurated"@en) -AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) -AnnotationAssertion(rdfs:label "uncurated"@en) - -# Individual: (pending final vetting) - -AnnotationAssertion( "pending final vetting"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "pending final vetting"@en) -ClassAssertion( ) - -# Individual: (to be replaced with external ontology term) - -AnnotationAssertion( "to be replaced with external ontology term"@en) -AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) - -# Individual: (requires discussion) - -AnnotationAssertion( "requires discussion"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "requires discussion"@en) -ClassAssertion( ) +# Class: (planned process) + +AnnotationAssertion( "planned process"@en) +AnnotationAssertion( "planned process") +AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") +AnnotationAssertion( ) +AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) +AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") +AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "branch derived") +AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) +AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "planned process"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (specimen role) + +AnnotationAssertion( "specimen role") +AnnotationAssertion( "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.") +AnnotationAssertion( ) +AnnotationAssertion( "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en) +AnnotationAssertion( "blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen."@en) +AnnotationAssertion( "parasite example +- when parasite in people we study people, people are subjects and parasites are specimen +- when parasite extracted, they become subject in the following study +specimen can later be subject."@en) +AnnotationAssertion( "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.") +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "GROUP: Role Branch") +AnnotationAssertion( "OBI") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "specimen role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) + +# Class: (specimen collection process) + +AnnotationAssertion( "specimen collection process") +AnnotationAssertion( "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective of collecting a specimen.") +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.") +AnnotationAssertion( "Philly2013: The specimen_role for the specimen is created during the specimen collection process.") +AnnotationAssertion( "label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "specimen collection") +AnnotationAssertion( "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession") +AnnotationAssertion( "6/9/09: used at workshop") +AnnotationAssertion(rdfs:label "specimen collection process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (specimen collection objective) + +AnnotationAssertion( "specimen collection objective") +AnnotationAssertion( "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.") +AnnotationAssertion( ) +AnnotationAssertion( "A objective specification to obtain a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion(rdfs:label "specimen collection objective") +SubClassOf( ) + +# Class: (collection of specimens) + +AnnotationAssertion( "collection of specimens"@en) +AnnotationAssertion( "Blood cells collected from multiple donors over the course of a study."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that has two or more specimens as its parts."@en) +AnnotationAssertion( "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/") +AnnotationAssertion( "Person: Chris Stoeckert, Jie Zheng"@en) +AnnotationAssertion( "OBIB, OBI") +AnnotationAssertion( "Biobank") +AnnotationAssertion(rdfs:label "collection of specimens"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) +SubClassOf( ) + +# Class: (specimen) + +AnnotationAssertion( "specimen"@en) +AnnotationAssertion( "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.") +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that has the specimen role."@en) +AnnotationAssertion( "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.") +AnnotationAssertion( "PERSON: James Malone") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "specimen"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) -DifferentIndividuals( ) +DisjointClasses( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -1856,6 +2249,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl deleted file mode 100644 index f7136c4..0000000 --- a/src/ontology/imports/obi_import.owl +++ /dev/null @@ -1,153 +0,0 @@ -Prefix(:=) -Prefix(owl:=) -Prefix(rdf:=) -Prefix(xml:=) -Prefix(xsd:=) -Prefix(rdfs:=) - - -Ontology( - -Annotation( "en") -Annotation( "Ontology for Biomedical Investigations"@en) -Annotation( "Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester"@en) -Annotation( "Alan Ruttenberg"@en) -Annotation( "Allyson Lister"@en) -Annotation( "Barry Smith"@en) -Annotation( "Bill Bug"@en) -Annotation( "Bjoern Peters"@en) -Annotation( "Carlo Torniai"@en) -Annotation( "Chris Mungall"@en) -Annotation( "Chris Stoeckert"@en) -Annotation( "Chris Taylor"@en) -Annotation( "Christian Bolling"@en) -Annotation( "Cristian Cocos"@en) -Annotation( "Daniel Rubin"@en) -Annotation( "Daniel Schober"@en) -Annotation( "Dawn Field"@en) -Annotation( "Dirk Derom"@en) -Annotation( "Elisabetta Manduchi"@en) -Annotation( "Eric Deutsch"@en) -Annotation( "Frank Gibson"@en) -Annotation( "Gilberto Fragoso"@en) -Annotation( "Helen C. Causton"@en) -Annotation( "Helen Parkinson"@en) -Annotation( "Holger Stenzhorn"@en) -Annotation( "James A. Overton"@en) -Annotation( "James Malone"@en) -Annotation( "Jay Greenbaum"@en) -Annotation( "Jeffrey Grethe"@en) -Annotation( "Jennifer Fostel"@en) -Annotation( "Jessica Turner"@en) -Annotation( "Jie Zheng"@en) -Annotation( "Joe White"@en) -Annotation( "John Westbrook"@en) -Annotation( "Kevin Clancy"@en) -Annotation( "Larisa Soldatova"@en) -Annotation( "Lawrence Hunter"@en) -Annotation( "Liju Fan"@en) -Annotation( "Luisa Montecchi"@en) -Annotation( "Matthew Brush"@en) -Annotation( "Matthew Pocock"@en) -Annotation( "Melanie Courtot"@en) -Annotation( "Melissa Haendel"@en) -Annotation( "Mervi Heiskanen"@en) -Annotation( "Monnie McGee"@en) -Annotation( "Norman Morrison"@en) -Annotation( "Philippe Rocca-Serra"@en) -Annotation( "Phillip Lord"@en) -Annotation( "Pierre Grenon"@en) -Annotation( "Richard Bruskiewich"@en) -Annotation( "Richard Scheuermann"@en) -Annotation( "Robert Stevens"@en) -Annotation( "Ryan R. Brinkman"@en) -Annotation( "Stefan Wiemann"@en) -Annotation( "Susanna-Assunta Sansone"@en) -Annotation( "Tanya Gray"@en) -Annotation( "Tina Hernandez-Boussard"@en) -Annotation( "Trish Whetzel"@en) -Annotation( "Yongqun He"@en) -Annotation( "2009-07-31"^^xsd:date) -Annotation( "An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation."@en) -Annotation( "OWL-DL"@en) -Annotation( ) -Annotation( "An ontology for the annotation of biomedical and functional genomics experiments."@en) -Annotation( "http://creativecommons.org/licenses/by/4.0/") -Annotation( "Ontology for Biomedical Investigations") -Annotation(rdfs:comment "Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.") -Annotation(owl:versionInfo "2023-07-25") -Annotation(owl:versionInfo "2023-08-15") - -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(Datatype(xsd:date)) - -############################ -# Object Properties -############################ - -# Object Property: (has_specified_input) - -AnnotationAssertion( "The inverse property of is_specified_input_of"@en) -AnnotationAssertion(rdfs:label "has_specified_input"@en) -EquivalentObjectProperties( ObjectInverseOf()) -SubObjectPropertyOf( ) - -# Object Property: (is_specified_input_of) - -AnnotationAssertion( "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en) -AnnotationAssertion(rdfs:label "is_specified_input_of"@en) -SubObjectPropertyOf( ) - -# Object Property: (has_specified_output) - -AnnotationAssertion( "The inverse property of is_specified_output_of"@en) -AnnotationAssertion(rdfs:label "has_specified_output"@en) -EquivalentObjectProperties( ObjectInverseOf()) -SubObjectPropertyOf( ) - -# Object Property: (is_specified_output_of) - -AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) -AnnotationAssertion(rdfs:label "is_specified_output_of"@en) -SubObjectPropertyOf( ) - -# Object Property: (achieves_planned_objective) - -AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.") -AnnotationAssertion(rdfs:label "achieves_planned_objective") - -# Object Property: (objective_achieved_by) - -AnnotationAssertion( "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.") -AnnotationAssertion(rdfs:label "objective_achieved_by") - - - -) \ No newline at end of file diff --git a/src/ontology/vfbext-edit.owl b/src/ontology/vfbext-edit.owl index 5156e91..4cee3ba 100644 --- a/src/ontology/vfbext-edit.owl +++ b/src/ontology/vfbext-edit.owl @@ -12,10 +12,7 @@ Prefix(oboInOwl:=) Ontology( -Import() -Import() -Import() -Import() +Import() Annotation( "An ontology of miscellaneous terms for data annotation in VFB.") Annotation( "VFB Extension Ontology") Annotation(terms:license "https://creativecommons.org/licenses/by/4.0/") diff --git a/src/ontology/vfbext-odk.yaml b/src/ontology/vfbext-odk.yaml index 78f30b5..3d7b1c9 100644 --- a/src/ontology/vfbext-odk.yaml +++ b/src/ontology/vfbext-odk.yaml @@ -18,13 +18,22 @@ export_formats: - obo - json import_group: + use_base_merging: TRUE + slme_individuals: exclude + release_imports: TRUE products: - id: ro + use_base: TRUE - id: caro - module_type: custom + make_base: TRUE + base_iris: + - http://purl.obolibrary.org/obo/CARO_ - id: fbbt + use_base: TRUE - id: obi - module_type: minimal + make_base: TRUE + base_iris: + - http://purl.obolibrary.org/obo/OBI_ edit_format: owl robot_java_args: '-Xmx8G' allow_equivalents: all diff --git a/src/ontology/vfbext.Makefile b/src/ontology/vfbext.Makefile index 9bb52c0..1c3fdd6 100644 --- a/src/ontology/vfbext.Makefile +++ b/src/ontology/vfbext.Makefile @@ -3,24 +3,12 @@ ## If you need to customize your Makefile, make ## changes here rather than in the main Makefile -# Include copying import files -.PHONY: prepare_release -prepare_release: $(ASSETS) - rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ - rsync -R $(IMPORT_FILES) $(RELEASEDIR) &&\ - rm -f $(CLEANFILES) &&\ - rm -f imports/*_terms_combined.txt &&\ - echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab" +# remove _terms_combined files +CLEANFILES := $(CLEANFILES) imports/*_terms_combined.txt + # Add VFB iri $(ONT).owl: $(ONT)-full.owl grep -v owl:versionIRI $< > $@.tmp.owl $(ROBOT) annotate --input $@.tmp.owl --ontology-iri http://virtualflybrain.org/data/VFB/OWL/vfbext.owl \ convert -o $@.tmp.owl && mv $@.tmp.owl $@ - -# smaller CARO import -$(IMPORTDIR)/caro_import.owl: $(MIRRORDIR)/caro.owl - if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ - extract --method MIREOT --force true --copy-ontology-annotations true \ - --lower-term "obo:CARO_0030002" \ - annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi diff --git a/vfbext-base.json b/vfbext-base.json index 899d75c..22c7cdb 100644 --- a/vfbext-base.json +++ b/vfbext-base.json @@ -16,15 +16,15 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "15:08:2023 10:37" + "val" : "26:10:2023 13:58" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-15" + "val" : "2023-10-26" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-08-15/vfbext-base.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-10-26/vfbext-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", @@ -155,6 +155,10 @@ "type" : "PROPERTY" } ], "edges" : [ { + "sub" : "http://purl.obolibrary.org/obo/SO_0000110", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { "sub" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" diff --git a/vfbext-base.obo b/vfbext-base.obo index 4dca6fa..8127524 100644 --- a/vfbext-base.obo +++ b/vfbext-base.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2023-08-15/vfbext-base.owl -date: 15:08:2023 10:37 +data-version: vfbext/releases/2023-10-26/vfbext-base.owl +date: 26:10:2023 13:58 subsetdef: clone "" subsetdef: neuron "" subsetdef: ns_part "" @@ -12,7 +12,11 @@ property_value: http://purl.org/dc/elements/1.1/description "An ontology of misc property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2023-08-15" xsd:string +property_value: owl:versionInfo "2023-10-26" xsd:string + +[Term] +id: SO:0000110 +is_a: BFO:0000040 [Term] id: VFB:10000005 diff --git a/vfbext-base.owl b/vfbext-base.owl index fae8c4d..2b506cb 100644 --- a/vfbext-base.owl +++ b/vfbext-base.owl @@ -11,17 +11,16 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:vfb2="http://purl.obolibrary.org/obo/fbbt/vfb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 15:08:2023 10:37 + 26:10:2023 13:58 VFB extension ontology - 2023-08-15 + 2023-10-26 @@ -37,12 +36,6 @@ - - - - - - @@ -97,42 +90,12 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -169,12 +132,6 @@ - - - - - - @@ -211,23 +168,6 @@ - - - - - - - - - - - + + + + + @@ -381,6 +327,14 @@ + + + + + + + + @@ -460,5 +414,5 @@ - + diff --git a/vfbext-full.json b/vfbext-full.json index 62811d4..6179bf0 100644 --- a/vfbext-full.json +++ b/vfbext-full.json @@ -13,167 +13,24 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "15:08:2023 10:37" + "val" : "26:10:2023 13:58" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-15" + "val" : "2023-10-26" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-08-15/vfbext-full.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-10-26/vfbext-full.json" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000078", - "lbl" : "curation status specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "curation status specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bill Bug" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000266" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000001", - "lbl" : "entity", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "entity" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "Entity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Julius Caesar" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Verdi’s Requiem" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the Second World War" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "your body mass index" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "Continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", @@ -192,62 +49,7 @@ "definition" : { "val" : "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])" }, - "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "ic" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "IndependentContinuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a chair" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a heart" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a leg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a molecule" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a spatial region" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an atom" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an orchestra." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an organism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the bottom right portion of a human torso" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the interior of your mouth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(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] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", @@ -320,18 +122,13 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a part and its whole" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - }, { - "val" : "OBO_REL:part_of" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is part of" @@ -380,15 +177,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "relationship" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" @@ -405,18 +193,13 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a whole and its part" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - }, { - "val" : "OBO_REL:has_part" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has part" @@ -444,15 +227,64 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "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" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realized in" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease is realized in this disease course" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "relationship" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is realized in this shattering" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is realized in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is realized by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "realized_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "[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])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "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" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realizes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease course realizes this disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation realizes this investigator role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this shattering realizes this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "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])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { @@ -477,7 +309,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } @@ -515,1383 +347,727 @@ "comments" : [ "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure." ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000006", - "lbl" : "material anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000003", + "lbl" : "connected anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical entity that has mass." + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." }, + "comments" : [ "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development." ], "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000007", - "lbl" : "immaterial anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000004", + "lbl" : "organism substance", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that has no mass." + "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." }, - "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] + "comments" : [ "Note - CARO explicitly declares organisms substances to be part of (some) organism." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "portion of organism substance" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle." + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0020003", - "lbl" : "cellular anatomical structure", + "id" : "http://purl.obolibrary.org/obo/CARO_0000006", + "lbl" : "material anatomical entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure consisting of one or more cells." + "val" : "An anatomical entity that has mass." }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-09-28T14:20:19Z" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0030000", - "lbl" : "biological entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000007", + "lbl" : "immaterial anatomical entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." + "val" : "Anatomical entity that has no mass." }, - "comments" : [ "Important for alignment with Darwin Core class \"Organism\"." ] + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0030002", - "lbl" : "expression pattern", + "id" : "http://purl.obolibrary.org/obo/CARO_0000012", + "lbl" : "multicellular organism", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." - } + "val" : "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." + }, + "comments" : [ "MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. \n\nMH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities." ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_00007001", - "lbl" : "anatomical structure", + "id" : "http://purl.obolibrary.org/obo/CARO_0000013", + "lbl" : "cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.", - "xrefs" : [ "CARO:MAH", "FBC:DOS" ] + "val" : "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." }, - "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], + "comments" : [ "deprecate and replace with CL or GO term?" ], "xrefs" : [ { - "val" : "CARO:0000003" + "val" : "CL:0000000" }, { - "val" : "UBERON:0000061" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "val" : "GO:0005623" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_00007016", - "lbl" : "material anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000014", + "lbl" : "cell part", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], - "xrefs" : [ { - "val" : "CARO:0000006" - }, { - "val" : "UBERON:0000465" - } ], + "definition" : { + "val" : "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." + }, + "comments" : [ "This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "cell component" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_00100313", - "lbl" : "multicellular structure", + "id" : "http://purl.obolibrary.org/obo/CARO_0000032", + "lbl" : "organism subdivision", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that has multiple cells as parts.", - "xrefs" : [ "FBC:DOS" ] + "val" : "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." }, - "xrefs" : [ { - "val" : "UBERON:0010000" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2010-11-02T02:25:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_10000000", - "lbl" : "anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000040", + "lbl" : "acellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity which is part_of Drosophila melanogaster.", - "xrefs" : [ "CARO:MAH" ] + "val" : "An anatomical structure that has no cells or cell parts as a part." }, - "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#EmbDevSlim", "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Drosophila" - } ], - "xrefs" : [ { - "val" : "UBERON:0001062" - } ], + "comments" : [ "Example. Insect cuticle, eggshell, hair." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000042", + "lbl" : "extraembryonic structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." + }, + "comments" : [ "MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: \"Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.\". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?\n" ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#plus" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001000", + "lbl" : "multi-cell-part structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." + }, + "comments" : [ "Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain." ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "FBbt_root:00000000" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-cell-component structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003674", - "lbl" : "molecular_function", + "id" : "http://purl.obolibrary.org/obo/CARO_0001008", + "lbl" : "gross anatomical part", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", - "xrefs" : [ "GOC:pdt" ] + "val" : "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecular function" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#plus" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005554" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "10.7.2011" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003824", - "lbl" : "catalytic activity", + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "lbl" : "organism", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.", - "xrefs" : [ "GOC:vw", "ISBN:0198506732" ] + "val" : "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "enzyme activity", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - } ], - "xrefs" : [ { - "val" : "Wikipedia:Enzyme" + "val" : "organism or virus or viroid" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Melissa Haendel" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "9/18/11" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0008150", - "lbl" : "biological_process", + "id" : "http://purl.obolibrary.org/obo/CARO_0010000", + "lbl" : "multicellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.", - "xrefs" : [ "GOC:pdt" ] + "val" : "An anatomical structure that has more than one cell as a part." }, - "comments" : [ "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." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "biological process" - }, { - "pred" : "hasExactSynonym", - "val" : "physiological process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single organism process" + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "djs93" }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism process" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Biological_process" - } ], + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Sun Feb 27 10:53:00 GMT 2011" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0010004", + "lbl" : "cellular organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An individual member of a clade of cellular organisms." + }, + "comments" : [ "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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. " ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/24968" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "7.16.2011" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0020000", + "lbl" : "disconnected anatomical group", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0020003", + "lbl" : "cellular anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure consisting of one or more cells." + }, + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" + "val" : "2018-09-28T14:20:19Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016301", - "lbl" : "kinase activity", + "id" : "http://purl.obolibrary.org/obo/CARO_0030000", + "lbl" : "biological entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", - "xrefs" : [ "ISBN:0198506732" ] + "val" : "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." }, - "comments" : [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "phosphokinase activity" - } ], + "comments" : [ "Important for alignment with Darwin Core class \"Organism\"." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0030002", + "lbl" : "expression pattern", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/FBbt_00007001", + "lbl" : "anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.", + "xrefs" : [ "https://orcid.org/0000-0001-9114-8737", "https://orcid.org/0000-0002-7073-9172" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], "xrefs" : [ { - "val" : "Reactome:R-HSA-6788855" + "val" : "CARO:0000003" }, { - "val" : "Reactome:R-HSA-6788867" + "val" : "UBERON:0000061" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "val" : "fly_anatomy.ontology" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016740", - "lbl" : "transferase activity", + "id" : "http://purl.obolibrary.org/obo/FBbt_00007016", + "lbl" : "material anatomical entity", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], "xrefs" : [ { - "val" : "EC:2.-.-.-" - }, { - "val" : "Reactome:R-HSA-1483089" - }, { - "val" : "Reactome:R-HSA-1483186" - }, { - "val" : "Reactome:R-HSA-5668414" + "val" : "CARO:0000006" }, { - "val" : "Reactome:R-HSA-8868783" + "val" : "UBERON:0000465" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "val" : "fly_anatomy.ontology" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016772", - "lbl" : "transferase activity, transferring phosphorus-containing groups", + "id" : "http://purl.obolibrary.org/obo/FBbt_00100313", + "lbl" : "multicellular structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).", - "xrefs" : [ "GOC:jl", "ISBN:0198506732" ] + "val" : "Anatomical structure that has multiple cells as parts.", + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, - "comments" : [ "Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "xrefs" : [ { - "val" : "EC:2.7.-.-" + "val" : "UBERON:0010000" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2010-11-02T02:25:04Z" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" + "val" : "fly_anatomy.ontology" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000112", - "lbl" : "example of usage", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/FBbt_10000000", + "lbl" : "anatomical entity", + "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Anatomical entity which is part_of Drosophila melanogaster.", + "xrefs" : [ "https://orcid.org/0000-0001-9114-8737" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#EmbDevSlim", "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "Drosophila" + } ], "xrefs" : [ { - "val" : "IAO:0000112" + "val" : "UBERON:0001062" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "FBbt_root:00000000" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "example_of_usage" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "fly_anatomy.ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "lbl" : "definition", - "type" : "PROPERTY", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "lbl" : "planned process", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." + "val" : "A process that realizes a plan which is the concretization of a plan specification." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Injecting mice with a vaccine in order to test its efficacy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " + "val" : "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" + "val" : "Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "branch derived" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "6/11/9: Edited at workshop. Used to include: is initiated by an agent" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000112", + "lbl" : "specimen role", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "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." + "val" : "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" + "val" : "specimen role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "blood taken from animal: animal continues in study, whereas blood has role specimen.\nsomething taken from study subject, leaves the study and becomes the specimen." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "parasite example\n- when parasite in people we study people, people are subjects and parasites are specimen\n- when parasite extracted, they become subject in the following study\nspecimen can later be subject." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP: Role Branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obi-ontology/obi/issues/1013" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "lbl" : "has_specified_input", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + "val" : "The inverse property of is_specified_input_of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "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.\"" - }, - "basicPropertyValues" : [ { + "val" : "has_specified_input" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" + "val" : "has_specified_input" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "see is_input_of example_of_usage" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Larry Hunter" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Coutot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000295", + "lbl" : "is_specified_input_of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. 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However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Philly2013: The specimen_role for the specimen is created during the specimen collection process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "label changed to 'specimen collection process' on 10/27/2014, details see tracker:\nhttp://sourceforge.net/p/obi/obi-terms/716/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "specimen collection" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "6/9/09: used at workshop" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001018", - "lbl" : "physical quality", + "id" : "http://purl.obolibrary.org/obo/OBI_0000684", + "lbl" : "specimen collection objective", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.", - "xrefs" : [ "PATOC:GVG" ] + "val" : "A objective specification to obtain a material entity for potential use as an input during an investigation." }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "relational physical quality" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Physical_property" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "specimen collection objective" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Bjoern Peters" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001241", - "lbl" : "physical object quality", + "id" : "http://purl.obolibrary.org/obo/OBI_0002076", + "lbl" : "collection of specimens", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A quality which inheres in a continuant.", - "xrefs" : [ "PATOC:GVG" ] + "val" : "A material entity that has two or more specimens as its parts." }, - "comments" : [ "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." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "monadic quality of a continuant" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "collection of specimens" }, { - "pred" : "hasExactSynonym", - "val" : "multiply inhering quality of a physical entity" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Blood cells collected from multiple donors over the course of a study." }, { - "pred" : "hasExactSynonym", - "val" : "multiply inhering quality of a physical entity " + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "hasExactSynonym", - "val" : "quality of a continuant" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/" }, { - "pred" : "hasExactSynonym", - "val" : "quality of a single physical entity" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Chris Stoeckert, Jie Zheng" }, { - "pred" : "hasExactSynonym", - "val" : "quality of an object" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBIB, OBI" }, { - "pred" : "hasExactSynonym", - "val" : "quality of continuant" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "Biobank" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0100051", + "lbl" : "specimen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that has the specimen role." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "specimen" }, { - "pred" : "hasNarrowSynonym", - "val" : "monadic quality of an object" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." }, { - "pred" : "hasNarrowSynonym", - "val" : "monadic quality of continuant" - } ], - "xrefs" : [ { - "val" : "snap:Quality" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: James Malone" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Philippe Rocca-Serra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP: OBI Biomaterial Branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obi-ontology/obi/issues/1013" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic_of", + "lbl" : "characteristic of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." }, "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], - "xrefs" : [ { - "val" : "RO:0000052" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "inheres in" @@ -1907,25 +1083,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "characteristic_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has_characteristic", + "lbl" : "has characteristic", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of characteristic_of" }, - "xrefs" : [ { - "val" : "RO:0000053" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "bearer of" @@ -1947,12 +1114,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_characteristic" } ] } }, { @@ -2007,10 +1168,42 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "lbl" : "is concretized as", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "lbl" : "concretizes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000079", "lbl" : "function of", @@ -2379,9 +1572,6 @@ "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002131" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -2391,12 +1581,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "overlaps" } ] } }, { @@ -2453,9 +1637,6 @@ "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002211" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-7476-6306" @@ -2480,9 +1661,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "false" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "gene_ontology" } ] } }, { @@ -2494,9 +1672,6 @@ "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002212" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" @@ -2509,9 +1684,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "gene_ontology" } ] } }, { @@ -2523,9 +1695,6 @@ "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002213" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" @@ -2538,23 +1707,17 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "gene_ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable_of", + "lbl" : "capable of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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. " }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002215" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" @@ -2576,37 +1739,22 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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)\"." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002216", - "lbl" : "capable_of_part_of", + "lbl" : "capable of part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, - "xrefs" : [ { - "val" : "RO:0002216" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function in" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of_part_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -2705,21 +1853,12 @@ "definition" : { "val" : "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." }, - "xrefs" : [ { - "val" : "RO:0002292" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "expresses" } ] } }, { @@ -3687,19 +2826,6 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002610", - "lbl" : "correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Groups both positive and negative correlation" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "lbl" : "directly positively regulates", @@ -3746,6 +2872,22 @@ "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004031", "lbl" : "enables subfunction", @@ -3838,52 +2980,145 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:53:22Z" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" + "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004046", - "lbl" : "causally upstream of or within, negative effect", + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "lbl" : "generically depends on", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "g-depends on" + } ], 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"http://purl.obolibrary.org/obo/NCBITaxon_7147" + "obj" : "http://purl.obolibrary.org/obo/FBbt_00007001" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7214", + "sub" : "http://purl.obolibrary.org/obo/FBbt_10000000", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_43746" + "obj" : "http://purl.obolibrary.org/obo/CARO_0000000" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7215", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_46877" + "sub" : "http://purl.obolibrary.org/obo/FBbt_10000000", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7227", + "sub" : "http://purl.obolibrary.org/obo/OBI_0000011", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_32351" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_7496", + "sub" : "http://purl.obolibrary.org/obo/OBI_0000112", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_85512" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_85512", + "sub" : "http://purl.obolibrary.org/obo/OBI_0000659", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_50557" + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_88770", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1206794" + "sub" : "http://purl.obolibrary.org/obo/OBI_0000659", + "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000001", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + "sub" : "http://purl.obolibrary.org/obo/OBI_0000659", + "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100051" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000125", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" + "sub" : "http://purl.obolibrary.org/obo/OBI_0000659", + "pred" : "http://purl.obolibrary.org/obo/OBI_0000417", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000684" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001018", + "sub" : "http://purl.obolibrary.org/obo/OBI_0000684", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" + "obj" : "http://purl.obolibrary.org/obo/IAO_0000005" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001241", + "sub" : "http://purl.obolibrary.org/obo/OBI_0002076", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "sub" : "http://purl.obolibrary.org/obo/OBI_0100051", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" + "sub" : "http://purl.obolibrary.org/obo/OBI_0100051", + "pred" : "http://purl.obolibrary.org/obo/RO_0000087", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000112" }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "sub" : "http://purl.obolibrary.org/obo/SO_0000110", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", "pred" : "is_a", @@ -4564,14 +3649,6 @@ "sub" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", "pred" : "is_a", "obj" : "http://xmlns.com/foaf/0.1/image" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000428", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "subPropertyOf", @@ -5028,6 +4105,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002630", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004028", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002410" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004031", "pred" : "subPropertyOf", @@ -5064,6 +4145,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004047", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0009501", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002410" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011002", "pred" : "subPropertyOf", @@ -5080,10 +4165,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0017003", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002610" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0019000", "pred" : "subPropertyOf", @@ -5116,6 +4197,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000055" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000062", "pred" : "inverseOf", @@ -5128,6 +4213,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000056", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000058", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000059" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000079", "pred" : "inverseOf", @@ -5208,14 +4297,35 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002559", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002566" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0010001", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0010002" } ], "logicalDefinitionAxioms" : [ { + "definedClassId" : "http://purl.obolibrary.org/obo/CARO_0000003", + "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0002266" + }, { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0010000" + } ] + }, { "definedClassId" : "http://purl.obolibrary.org/obo/CARO_0000006", "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000125" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CARO_0010000", + "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001993" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/FBbt_10000000", "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], @@ -5223,6 +4333,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0000659", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000417", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000684" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0100051", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000112" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004", "genusIds" : [ "http://purl.obolibrary.org/obo/FBbt_00100313" ], @@ -5262,6 +4386,14 @@ "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000055", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000062", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -5278,6 +4410,14 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000059", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ] @@ -5360,6 +4500,22 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0011002", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -5396,6 +4552,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000055", "http://purl.obolibrary.org/obo/RO_0000052" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -5405,9 +4564,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002584", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000054", "http://purl.obolibrary.org/obo/RO_0002404" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/RO_0000058" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -5540,6 +4708,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] } ] } ] } \ No newline at end of file diff --git a/vfbext-full.obo b/vfbext-full.obo index 41e2548..bd6ea42 100644 --- a/vfbext-full.obo +++ b/vfbext-full.obo @@ -1,24 +1,10 @@ format-version: 1.2 -data-version: vfbext/releases/2023-08-15/vfbext-full.owl -date: 15:08:2023 10:37 -subsetdef: attribute_slim "" +data-version: vfbext/releases/2023-10-26/vfbext-full.owl +date: 26:10:2023 13:58 subsetdef: clone "" -subsetdef: common_anatomy "" subsetdef: core "" subsetdef: cur "" subsetdef: EmbDevSlim "" -subsetdef: goslim_agr "" -subsetdef: goslim_candida "" -subsetdef: goslim_chembl "" -subsetdef: goslim_drosophila "" -subsetdef: goslim_flybase_ribbon "" -subsetdef: goslim_generic "" -subsetdef: goslim_metagenomics "" -subsetdef: goslim_mouse "" -subsetdef: goslim_pir "" -subsetdef: goslim_plant "" -subsetdef: goslim_pombe "" -subsetdef: goslim_yeast "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -26,96 +12,40 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: larval_OF "" subsetdef: neuron "" subsetdef: ns_part "" -subsetdef: prokaryote_subset "" -subsetdef: relational_slim "" +subsetdef: plus "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" -subsetdef: scalar_slim "" subsetdef: synaptic_neuropil "" subsetdef: tract "" -subsetdef: upper_level "" -synonymtypedef: blast_name "" -synonymtypedef: common_name "" -synonymtypedef: genbank_common_name "" -synonymtypedef: in_part "" -synonymtypedef: scientific_name "" -synonymtypedef: synonym "" remark: VFB extension ontology ontology: vfbext/vfbext-full property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2023-08-15" xsd:string - -[Term] -id: BFO:0000001 -name: entity -property_value: BFO:0000179 "entity" xsd:string -property_value: BFO:0000180 "Entity" xsd:string -property_value: editor_note "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: editor_note "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: example_of_usage "Julius Caesar" xsd:string -property_value: example_of_usage "the Second World War" xsd:string -property_value: example_of_usage "Verdi’s Requiem" xsd:string -property_value: example_of_usage "your body mass index" xsd:string -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 +property_value: owl:versionInfo "2023-10-26" xsd:string [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." [] -is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: part_of BFO:0000002 {all_only="true"} ! continuant -property_value: BFO:0000179 "continuant" xsd:string -property_value: BFO:0000180 "Continuant" xsd:string -property_value: editor_note "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: editor_note "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 +relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: part_of BFO:0000003 {all_only="true"} ! occurrent +relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent [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." [] -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"} +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])" [] comment: 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 disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant -property_value: BFO:0000179 "ic" xsd:string -property_value: BFO:0000180 "IndependentContinuant" xsd:string -property_value: example_of_usage "a chair" xsd:string -property_value: example_of_usage "a heart" xsd:string -property_value: example_of_usage "a leg" xsd:string -property_value: example_of_usage "a molecule" xsd:string -property_value: example_of_usage "a spatial region" xsd:string -property_value: example_of_usage "an atom" xsd:string -property_value: example_of_usage "an orchestra." xsd:string -property_value: example_of_usage "an organism" xsd:string -property_value: example_of_usage "the bottom right portion of a human torso" xsd:string -property_value: example_of_usage "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 +relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant [Term] id: BFO:0000015 @@ -136,13 +66,13 @@ name: realizable entity def: "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." [] is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality -relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity +relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant -relationship: part_of BFO:0000019 {all_only="true"} ! quality +relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 @@ -151,7 +81,7 @@ def: "b is a specifically dependent continuant = Def. b is a continuant & there comment: 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 disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant [Term] id: BFO:0000023 @@ -165,7 +95,7 @@ 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])" [] comment: 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. is_a: BFO:0000002 ! continuant -relationship: part_of BFO:0000031 {all_only="true"} ! generically dependent continuant +relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant [Term] id: BFO:0000034 @@ -191,6 +121,29 @@ def: "A part of a cellular organism that is either an immaterial entity or a mat comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. is_a: CARO:0030000 ! biological entity +[Term] +id: CARO:0000003 +name: connected anatomical structure +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [] +comment: Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. +subset: core +is_a: CARO:0000006 ! material anatomical entity +intersection_of: CARO:0000006 ! material anatomical entity +intersection_of: RO:0000053 PATO:0002266 ! has characteristic +intersection_of: RO:0000053 PATO:0010000 ! has characteristic +disjoint_from: CARO:0000004 ! organism substance +relationship: RO:0000053 PATO:0002266 ! has characteristic +relationship: RO:0000053 PATO:0010000 ! has characteristic + +[Term] +id: CARO:0000004 +name: organism substance +def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." [] +comment: Note - CARO explicitly declares organisms substances to be part of (some) organism. +synonym: "portion of organism substance" EXACT [] +is_a: CARO:0001008 ! gross anatomical part +property_value: IAO:0000112 "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle." xsd:string + [Term] id: CARO:0000006 name: material anatomical entity @@ -198,9 +151,9 @@ def: "An anatomical entity that has mass." [] subset: core is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity -intersection_of: has_characteristic PATO:0000125 ! mass +intersection_of: RO:0000053 PATO:0000125 ! has characteristic disjoint_from: CARO:0000007 ! immaterial anatomical entity -relationship: has_characteristic PATO:0000125 ! mass +relationship: RO:0000053 PATO:0000125 ! has characteristic [Term] id: CARO:0000007 @@ -210,6 +163,144 @@ subset: core is_a: BFO:0000141 ! immaterial entity is_a: CARO:0000000 ! anatomical entity +[Term] +id: CARO:0000012 +name: multicellular organism +def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] +comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. \n\nMH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. +is_a: CARO:0010004 ! cellular organism + +[Term] +id: CARO:0000013 +name: cell +def: "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [] +comment: deprecate and replace with CL or GO term? +xref: CL:0000000 +xref: GO:0005623 +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0020003 ! cellular anatomical structure +disjoint_from: CARO:0000014 ! cell part +disjoint_from: CARO:0000040 ! acellular anatomical structure +disjoint_from: CARO:0000042 ! extraembryonic structure +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure + +[Term] +id: CARO:0000014 +name: cell part +def: "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." [] +comment: This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class. +is_a: CARO:0000003 ! connected anatomical structure +disjoint_from: CARO:0000040 ! acellular anatomical structure +disjoint_from: CARO:0000042 ! extraembryonic structure +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 CARO:0000013 ! part of cell +property_value: IAO:0000118 "cell component" xsd:string + +[Term] +id: CARO:0000032 +name: organism subdivision +def: "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [] +subset: core +is_a: CARO:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." xsd:string + +[Term] +id: CARO:0000040 +name: acellular anatomical structure +def: "An anatomical structure that has no cells or cell parts as a part." [] +comment: Example. Insect cuticle, eggshell, hair. +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001008 ! gross anatomical part +intersection_of: CARO:0000003 ! connected anatomical structure +intersection_of: RO:0002180 CARO:0000013 {cardinality="0"} ! has component cell +intersection_of: RO:0002180 CARO:0000014 {cardinality="0"} ! has component cell part +disjoint_from: CARO:0000042 ! extraembryonic structure +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure + +[Term] +id: CARO:0000042 +name: extraembryonic structure +def: "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." [] +comment: MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?\n +subset: plus +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001008 ! gross anatomical part +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure + +[Term] +id: CARO:0001000 +name: multi-cell-part structure +def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [] +comment: Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain. +subset: core +is_a: CARO:0001008 ! gross anatomical part +disjoint_from: CARO:0010000 ! multicellular anatomical structure +property_value: IAO:0000118 "multi-cell-component structure" xsd:string + +[Term] +id: CARO:0001008 +name: gross anatomical part +def: "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " [] +subset: plus +is_a: CARO:0000006 ! material anatomical entity +union_of: CARO:0000004 ! organism substance +union_of: CARO:0000032 ! organism subdivision +union_of: CARO:0000040 ! acellular anatomical structure +union_of: CARO:0000042 ! extraembryonic structure +union_of: CARO:0001000 ! multi-cell-part structure +union_of: CARO:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 CARO:0000012 ! part of multicellular organism +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.7.2011" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 + +[Term] +id: CARO:0001010 +name: organism +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +synonym: "organism or virus or viroid" EXACT [] +is_a: BFO:0000040 ! material entity +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000117 "Melissa Haendel" xsd:string + +[Term] +id: CARO:0010000 +name: multicellular anatomical structure +def: "An anatomical structure that has more than one cell as a part." [] +subset: core +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001008 ! gross anatomical part +intersection_of: CARO:0000003 {comment="There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS"} ! connected anatomical structure +intersection_of: RO:0000053 PATO:0001993 {comment="There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS"} ! has characteristic +relationship: RO:0000053 PATO:0001993 ! has characteristic +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Sun Feb 27 10:53:00 GMT 2011" xsd:string +property_value: IAO:0000117 "djs93" xsd:string + +[Term] +id: CARO:0010004 +name: cellular organism +def: "An individual member of a clade of cellular organisms." [] +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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001010 ! organism +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 + +[Term] +id: CARO:0020000 +name: disconnected anatomical group +def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [] +subset: core +is_a: CARO:0000006 ! material anatomical entity +intersection_of: CARO:0000006 ! material anatomical entity +intersection_of: RO:0000053 PATO:0010001 ! has characteristic +intersection_of: RO:0002180 CARO:0000003 {minCardinality="2"} ! has component connected anatomical structure +relationship: RO:0000053 PATO:0010001 ! has characteristic +relationship: RO:0002180 CARO:0000003 ! has component connected anatomical structure + [Term] id: CARO:0020003 name: cellular anatomical structure @@ -230,12 +321,13 @@ id: CARO:0030002 name: expression pattern def: "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." [] is_a: CARO:0020003 ! cellular anatomical structure +relationship: BFO:0000051 CARO:0000013 ! has part cell [Term] id: FBbt:00007001 name: anatomical structure namespace: fly_anatomy.ontology -def: "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome." [CARO:MAH, FBC:DOS] +def: "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome." [https://orcid.org/0000-0001-9114-8737, https://orcid.org/0000-0002-7073-9172] subset: cur subset: larval_OF xref: CARO:0000003 @@ -256,10 +348,10 @@ is_a: FBbt:10000000 ! anatomical entity id: FBbt:00100313 name: multicellular structure namespace: fly_anatomy.ontology -def: "Anatomical structure that has multiple cells as parts." [FBC:DOS] +def: "Anatomical structure that has multiple cells as parts." [https://orcid.org/0000-0002-7073-9172] xref: UBERON:0010000 is_a: FBbt:00007001 ! anatomical structure -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 property_value: http://purl.org/dc/terms/date "2010-11-02T02:25:04Z" xsd:dateTime [Term] @@ -267,7 +359,7 @@ id: FBbt:10000000 name: anatomical entity namespace: fly_anatomy.ontology alt_id: FBbt_root:00000000 -def: "Anatomical entity which is part_of Drosophila melanogaster." [CARO:MAH] +def: "Anatomical entity which is part_of Drosophila melanogaster." [https://orcid.org/0000-0001-9114-8737] subset: cur subset: EmbDevSlim subset: larval_OF @@ -275,546 +367,118 @@ synonym: "Drosophila" RELATED [] xref: UBERON:0001062 is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity -intersection_of: part_of NCBITaxon:7227 ! Drosophila melanogaster -disjoint_from: PATO:0000001 ! quality -relationship: part_of NCBITaxon:7227 ! Drosophila melanogaster - -[Term] -id: GO:0003674 -name: molecular_function -namespace: molecular_function -alt_id: GO:0005554 -def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] -comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. -subset: goslim_candida -subset: goslim_chembl -subset: goslim_metagenomics -subset: goslim_pir -subset: goslim_plant -subset: goslim_yeast -synonym: "molecular function" EXACT [] - -[Term] -id: GO:0003824 -name: catalytic activity -namespace: molecular_function -def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732] -subset: goslim_agr -subset: goslim_chembl -subset: goslim_flybase_ribbon -subset: goslim_generic -subset: goslim_metagenomics -subset: goslim_pir -subset: goslim_plant -synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] -xref: Wikipedia:Enzyme -is_a: GO:0003674 ! molecular_function +intersection_of: BFO:0000050 NCBITaxon:7227 ! part of +disjoint_from: PATO:0000001 +relationship: BFO:0000050 NCBITaxon:7227 ! part of [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 is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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_candida -subset: goslim_chembl -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: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl -creation_date: 2012-09-19T15:05:24Z +disjoint_from: OBI:0000011 ! planned process [Term] id: GO:0016301 -name: kinase activity -namespace: molecular_function -def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] -comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_metagenomics -subset: goslim_plant -subset: goslim_yeast -synonym: "phosphokinase activity" EXACT [] -xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm" -xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines" -is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups - -[Term] -id: GO:0016740 -name: transferase activity -namespace: molecular_function -def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732] -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_generic -subset: goslim_metagenomics -subset: goslim_mouse -subset: goslim_pir -subset: goslim_plant -subset: goslim_yeast -subset: prokaryote_subset -xref: EC:2.-.-.- -xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2" -xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1" -xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK" -xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248" -is_a: GO:0003824 ! catalytic activity [Term] -id: GO:0016772 -name: transferase activity, transferring phosphorus-containing groups -namespace: molecular_function -def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] -comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. -subset: goslim_chembl -xref: EC:2.7.-.- -is_a: GO:0016740 ! transferase activity - -[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." [] -property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string -property_value: IAO:0000111 "curation status specification" xsd:string +id: OBI:0000011 +name: planned process +def: "A process that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string +property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000119 "branch derived" xsd:string +property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string +property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + +[Term] +id: OBI:0000112 +name: specimen role +def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] +is_a: BFO:0000023 ! role +property_value: IAO:0000111 "specimen role" xsd:string +property_value: IAO:0000112 "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role." xsd:string +property_value: IAO:0000116 "blood taken from animal: animal continues in study, whereas blood has role specimen.\nsomething taken from study subject, leaves the study and becomes the specimen." xsd:string +property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string +property_value: IAO:0000116 "parasite example\n- when parasite in people we study people, people are subjects and parasites are specimen\n- when parasite extracted, they become subject in the following study\nspecimen can later be subject." xsd:string +property_value: IAO:0000117 "GROUP: Role Branch" xsd:string +property_value: IAO:0000119 "OBI" xsd:string +property_value: IAO:0000233 https://github.com/obi-ontology/obi/issues/1013 + +[Term] +id: OBI:0000659 +name: specimen collection process +def: "A planned process with the objective of collecting a specimen." [] +is_a: OBI:0000011 ! planned process +intersection_of: OBI:0000011 ! planned process +intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective +relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity +relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen +relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective +property_value: IAO:0000111 "specimen collection process" xsd:string +property_value: IAO:0000112 "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "label changed to 'specimen collection process' on 10/27/2014, details see tracker:\nhttp://sourceforge.net/p/obi/obi-terms/716/" xsd:string +property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string +property_value: IAO:0000116 "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role." xsd:string +property_value: IAO:0000116 "Philly2013: The specimen_role for the specimen is created during the specimen collection process." xsd:string +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000118 "specimen collection" xsd:string +property_value: IAO:0000232 "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession" xsd:string +property_value: IAO:0000232 "6/9/09: used at workshop" xsd:string + +[Term] +id: OBI:0000684 +name: specimen collection objective +def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] +is_a: IAO:0000005 +property_value: IAO:0000111 "specimen collection objective" xsd:string +property_value: IAO:0000112 "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000119 "Bjoern Peters" xsd:string + +[Term] +id: OBI:0002076 +name: collection of specimens +def: "A material entity that has two or more specimens as its parts." [] +is_a: BFO:0000040 ! material entity +intersection_of: BFO:0000040 ! material entity +intersection_of: RO:0002351 OBI:0100051 {all_only="true"} ! has member specimen +property_value: http://purl.org/dc/elements/1.1/source "Biobank" xsd:string +property_value: IAO:0000111 "collection of specimens" xsd:string +property_value: IAO:0000112 "Blood cells collected from multiple donors over the course of a study." xsd:string property_value: IAO:0000114 IAO:0000125 -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: NCBITaxon:1 -name: root -namespace: ncbi_taxonomy -synonym: "all" RELATED synonym [] -xref: GC_ID:1 - -[Term] -id: NCBITaxon:1206794 -name: Ecdysozoa -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33317 ! Protostomia -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:131567 -name: cellular organisms -namespace: ncbi_taxonomy -synonym: "biota" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1 ! root - -[Term] -id: NCBITaxon:197562 -name: Pancrustacea -namespace: ncbi_taxonomy -xref: GC_ID:1 -xref: PMID:10874751 -xref: PMID:11557979 -is_a: NCBITaxon:197563 ! Mandibulata -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:197563 -name: Mandibulata -namespace: ncbi_taxonomy -synonym: "mandibulates" EXACT common_name [] -xref: GC_ID:1 -xref: PMID:11557979 -xref: PMID:9727836 -is_a: NCBITaxon:6656 ! Arthropoda -property_value: has_rank NCBITaxon:clade - -[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 -xref: PMID:30257078 -is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom - -[Term] -id: NCBITaxon:32341 -name: Sophophora -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7215 ! Drosophila -property_value: has_rank NCBITaxon:subgenus - -[Term] -id: NCBITaxon:32346 -name: melanogaster group -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:32341 ! Sophophora -property_value: has_rank NCBITaxon:species_group - -[Term] -id: NCBITaxon:32351 -name: melanogaster subgroup -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:32346 ! melanogaster group -property_value: has_rank NCBITaxon:species_subgroup - -[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: has_rank NCBITaxon:clade - -[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 - -[Term] -id: NCBITaxon:33213 -name: Bilateria -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:33317 -name: Protostomia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:33340 -name: Neoptera -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7496 ! Pterygota -property_value: has_rank NCBITaxon:infraclass - -[Term] -id: NCBITaxon:33392 -name: Endopterygota -namespace: ncbi_taxonomy -synonym: "Holometabola" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:33340 ! Neoptera -property_value: has_rank NCBITaxon:cohort - -[Term] -id: NCBITaxon:43733 -name: Muscomorpha -namespace: ncbi_taxonomy -alt_id: NCBITaxon:43732 -synonym: "Asilomorpha" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:7203 ! Brachycera -property_value: has_rank NCBITaxon:infraorder - -[Term] -id: NCBITaxon:43738 -name: Schizophora -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:480117 ! Cyclorrhapha - -[Term] -id: NCBITaxon:43741 -name: Acalyptratae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43738 ! Schizophora - -[Term] -id: NCBITaxon:43746 -name: Ephydroidea -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43741 ! Acalyptratae -property_value: has_rank NCBITaxon:superfamily - -[Term] -id: NCBITaxon:43845 -name: Drosophilinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7214 ! Drosophilidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:46877 -name: Drosophilini -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43845 ! Drosophilinae -property_value: has_rank NCBITaxon:tribe - -[Term] -id: NCBITaxon:480117 -name: Cyclorrhapha -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:480118 ! Eremoneura -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:480118 -name: Eremoneura -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43733 ! Muscomorpha -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:50557 -name: Insecta -namespace: ncbi_taxonomy -synonym: "insects" RELATED blast_name [] -synonym: "true insects" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:6960 ! Hexapoda -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:6072 -name: Eumetazoa -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade +property_value: IAO:0000116 "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/" xsd:string +property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string +property_value: IAO:0000119 "OBIB, OBI" xsd:string [Term] -id: NCBITaxon:6656 -name: Arthropoda -namespace: ncbi_taxonomy -synonym: "arthropods" EXACT genbank_common_name [] -synonym: "arthropods" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:88770 ! Panarthropoda -property_value: has_rank NCBITaxon:phylum - -[Term] -id: NCBITaxon:6960 -name: Hexapoda -namespace: ncbi_taxonomy -synonym: "Atelocerata" RELATED in_part [] -synonym: "hexapods" RELATED blast_name [] -synonym: "insects" EXACT genbank_common_name [] -synonym: "Tracheata" RELATED in_part [] -synonym: "Uniramia" RELATED in_part [] -xref: GC_ID:1 -is_a: NCBITaxon:197562 ! Pancrustacea -property_value: has_rank NCBITaxon:subphylum - -[Term] -id: NCBITaxon:7147 -name: Diptera -namespace: ncbi_taxonomy -synonym: "flies" EXACT genbank_common_name [] -synonym: "flies" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:33392 ! Endopterygota -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:7203 -name: Brachycera -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7147 ! Diptera -property_value: has_rank NCBITaxon:suborder - -[Term] -id: NCBITaxon:7214 -name: Drosophilidae -namespace: ncbi_taxonomy -synonym: "pomace flies" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:43746 ! Ephydroidea -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:7215 -name: Drosophila -namespace: ncbi_taxonomy -alt_id: NCBITaxon:7326 -synonym: "Drosophila" EXACT scientific_name [] -synonym: "fruit flies" EXACT genbank_common_name [] -synonym: "fruit fly" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:46877 ! Drosophilini -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:7227 -name: Drosophila melanogaster -namespace: ncbi_taxonomy -alt_id: NCBITaxon:2267365 -synonym: "fruit fly" EXACT genbank_common_name [] -synonym: "Sophophora melanogaster" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:32351 ! melanogaster subgroup -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:7496 -name: Pterygota -namespace: ncbi_taxonomy -synonym: "Pterygota" EXACT scientific_name [] -synonym: "winged insects" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:85512 ! Dicondylia -property_value: has_rank NCBITaxon:subclass - -[Term] -id: NCBITaxon:85512 -name: Dicondylia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:50557 ! Insecta -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:88770 -name: Panarthropoda -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1206794 ! Ecdysozoa -property_value: has_rank NCBITaxon:clade - -[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] -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 [] -is_a: BFO:0000020 ! specifically dependent continuant - -[Term] -id: PATO:0000125 -name: mass -namespace: quality -def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [PATOC:GVG] -comment: For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. -subset: attribute_slim -subset: relational_slim -subset: scalar_slim -is_a: PATO:0001018 ! physical quality - -[Term] -id: PATO:0001018 -name: physical quality -namespace: quality -alt_id: PATO:0002079 -def: "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] -subset: attribute_slim -synonym: "relational physical quality" EXACT [] -xref: Wikipedia:Physical_property -is_a: PATO:0001241 ! physical object quality - -[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: "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 - -[Term] -id: UBERON:0000465 -name: material anatomical entity -def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] -subset: common_anatomy -subset: upper_level -xref: AAO:0010264 -xref: AEO:0000006 -xref: BILA:0000006 -xref: CARO:0000006 -xref: EHDAA2:0003006 -xref: FBbt:00007016 -xref: FMA:67165 -xref: HAO:0000006 -xref: TAO:0001836 -xref: TGMA:0001826 -xref: VHOG:0001721 +id: OBI:0100051 +name: specimen +def: "A material entity that has the specimen role." [] +is_a: BFO:0000040 ! material entity +intersection_of: BFO:0000040 ! material entity +intersection_of: RO:0000087 OBI:0000112 ! has role specimen role +relationship: RO:0000087 OBI:0000112 ! has role specimen role +property_value: IAO:0000111 "specimen" xsd:string +property_value: IAO:0000112 "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string +property_value: IAO:0000117 "PERSON: James Malone" xsd:string +property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string +property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string +property_value: IAO:0000233 https://github.com/obi-ontology/obi/issues/1013 + +[Term] +id: SO:0000110 is_a: BFO:0000040 ! material entity -is_a: UBERON:0001062 ! anatomical entity -property_value: RO:0002175 NCBITaxon:33090 -property_value: RO:0002175 NCBITaxon:4751 - -[Term] -id: UBERON:0001062 -name: anatomical entity -def: "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." [FMA:62955, http://orcid.org/0000-0001-9114-8737] -subset: common_anatomy -subset: upper_level -xref: AAO:0010841 -xref: AEO:0000000 -xref: BILA:0000000 -xref: BIRNLEX:6 -xref: CARO:0000000 -xref: EHDAA2:0002229 -xref: FBbt:10000000 -xref: FMA:62955 -xref: HAO:0000000 -xref: MA:0000001 -xref: NCIT:C12219 -xref: TAO:0100000 -xref: TGMA:0001822 -xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} -xref: WBbt:0000100 -xref: XAO:0000000 -xref: ZFA:0100000 -is_a: BFO:0000004 ! independent continuant -property_value: RO:0002175 NCBITaxon:33090 -property_value: RO:0002175 NCBITaxon:4751 [Term] id: VFB:10000005 @@ -827,8 +491,8 @@ name: expression pattern fragment comment: A multicellular structure that is part of an expression pattern. is_a: FBbt:00100313 ! multicellular structure intersection_of: FBbt:00100313 ! multicellular structure -intersection_of: part_of CARO:0030002 ! expression pattern -relationship: part_of CARO:0030002 ! expression pattern +intersection_of: BFO:0000050 CARO:0030002 ! part of expression pattern +relationship: BFO:0000050 CARO:0030002 ! part of expression pattern created_by: dos creation_date: 2018-03-04T10:55:59Z @@ -857,19 +521,99 @@ id: VFBext:0000014 name: channel is_a: http://xmlns.com/foaf/0.1/image +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: 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 +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI +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" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: BFO:0000054 +name: realized in +comment: 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 +property_value: IAO:0000111 "realized in" xsd:string +property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string +property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string +property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string +property_value: IAO:0000118 "is realized by" xsd:string +property_value: IAO:0000118 "realized_in" xsd:string +property_value: IAO:0000600 "[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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +inverse_of: BFO:0000055 ! realizes + +[Typedef] +id: BFO:0000055 +name: realizes +comment: 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 +property_value: IAO:0000111 "realizes" xsd:string +property_value: IAO:0000112 "this disease course realizes this disease" xsd:string +property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string +property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string +property_value: IAO:0000600 "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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +domain: BFO:0000015 ! process +range: BFO:0000017 ! realizable entity + [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: editor_note "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: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/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 domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000062 +holds_over_chain: BFO:0000050 BFO:0000062 is_transitive: true is_a: RO:0002086 ! ends after inverse_of: BFO:0000063 ! precedes @@ -882,7 +626,7 @@ subset: ro-eco property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000063 +holds_over_chain: BFO:0000050 BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to @@ -890,44 +634,102 @@ is_a: RO:0002222 ! temporally related to id: OBI:0000293 name: has_specified_input def: "The inverse property of is_specified_input_of" [] +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl is_a: RO:0000057 ! has participant [Typedef] id: OBI:0000295 name: is_specified_input_of def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "is_specified_input_of" xsd:string +property_value: IAO:0000112 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl is_a: RO:0000057 ! has participant [Typedef] id: OBI:0000312 name: is_specified_output_of def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] +property_value: IAO:0000111 "achieves_planned_objective" xsd:string +property_value: IAO:0000112 "A cell sorting process achieves the objective specification 'material separation objective'" xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "BP, AR, PPPB branch" xsd:string +property_value: IAO:0000119 "PPPB branch derived" xsd:string +property_value: IAO:0000232 "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" xsd:string [Typedef] -id: OBI:0000833 -name: objective_achieved_by -def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] +id: RO:0000052 +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: RO:0002314 ! characteristic of part of +inverse_of: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000053 +name: has characteristic +def: "Inverse of characteristic_of" [] +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: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant +is_inverse_functional: true [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: example_of_usage "this blood clot participates in this blood coagulation" xsd:string -property_value: example_of_usage "this input material (or this output material) participates in this process" xsd:string -property_value: example_of_usage "this investigator participates in this investigation" xsd:string 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 domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent @@ -937,28 +739,47 @@ inverse_of: RO:0000057 ! has participant 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: editor_note "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: example_of_usage "this blood coagulation has participant this blood clot" xsd:string -property_value: example_of_usage "this investigation has participant this investigator" xsd:string -property_value: example_of_usage "this process has participant this input material (or this output material)" xsd:string -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/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 domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant -holds_over_chain: has_part RO:0000057 +holds_over_chain: BFO:0000051 RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant [Typedef] id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function [Typedef] @@ -966,11 +787,11 @@ 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" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: example_of_usage "this red color is a quality of this apple" xsd:string +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 -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of inverse_of: RO:0000086 ! has quality [Typedef] @@ -978,44 +799,44 @@ id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this investigator role is a role of this person" xsd:string +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role [Typedef] id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic [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: editor_note "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: example_of_usage "this apple has quality this red color" xsd:string +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 range: BFO:0000019 ! quality -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000091 @@ -1023,7 +844,7 @@ name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic inverse_of: RO:0000092 ! disposition of [Typedef] @@ -1032,7 +853,7 @@ name: disposition of def: "inverse of has disposition" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. subset: RO:0002259 -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of [Typedef] id: RO:0002013 @@ -1158,40 +979,55 @@ property_value: IAO:0000118 "meets" xsd:string 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: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: RO:0001900 RO:0001901 +holds_over_chain: BFO:0000050 BFO:0000050 +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} +holds_over_chain: BFO:0000051 RO:0002131 +is_symmetric: true +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: editor_note "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: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: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002206 name: expressed in def: "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" [] -property_value: example_of_usage "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string +property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant -range: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 is_a: RO:0002330 ! genomically related to -inverse_of: expresses ! expresses -transitive_over: part_of ! part_of +inverse_of: RO:0002292 ! expresses +transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002211 name: regulates -namespace: gene_ontology def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002211 property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -1211,12 +1047,10 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively regulates -namespace: gene_ontology def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002212 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string @@ -1228,12 +1062,10 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -namespace: gene_ontology def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002213 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -1244,6 +1076,33 @@ 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 https://orcid.org/0000-0002-6601-2165 +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 +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of + +[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 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + [Typedef] id: RO:0002222 name: temporally related to @@ -1278,7 +1137,7 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: example_of_usage "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: 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: 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 @@ -1289,11 +1148,19 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: example_of_usage "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: 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: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002292 +name: expresses +def: "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002330 ! genomically related to + [Typedef] id: RO:0002304 name: causally upstream of, positive effect @@ -1323,15 +1190,15 @@ is_a: RO:0004046 ! causally upstream of or within, negative effect id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: characteristic_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002323 @@ -1346,7 +1213,7 @@ id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string @@ -1355,9 +1222,9 @@ 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: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI -is_a: capable_of ! capable_of +is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by -transitive_over: has_part ! has part +transitive_over: BFO:0000051 ! has part transitive_over: RO:0002017 ! has component activity [Typedef] @@ -1373,7 +1240,7 @@ 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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -1393,10 +1260,10 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI -holds_over_chain: RO:0002327 part_of +holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002333 @@ -1440,12 +1307,12 @@ is_a: RO:0002334 ! regulated by id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: example_of_usage "An organism that is a member of a population of organisms" xsd:string +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: RO:0001900 RO:0001901 -is_a: part_of ! part_of +is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] @@ -1454,7 +1321,7 @@ 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: RO:0001900 RO:0001901 -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002352 @@ -1520,7 +1387,7 @@ transitive_over: RO:0002630 ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 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 @@ -1549,7 +1416,7 @@ id: RO:0002418 name: causally upstream of or within def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true @@ -1600,7 +1467,7 @@ is_a: RO:0002428 ! involved in regulation of 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: editor_note "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -1614,8 +1481,8 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 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: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI @@ -1638,7 +1505,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 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 is_a: RO:0002436 ! molecularly interacts with @@ -1719,7 +1586,7 @@ property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 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 @@ -1780,9 +1647,9 @@ is_a: RO:0002412 ! immediately causally upstream of 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: example_of_usage "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: has_part capable_of +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 @@ -1790,7 +1657,7 @@ is_a: RO:0002595 ! causal relation between material entity and a process 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: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity @@ -1801,9 +1668,9 @@ is_a: RO:0002410 ! causally related to 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: example_of_usage "pyrethroid -> growth" xsd:string +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -holds_over_chain: capable_of RO:0002211 +holds_over_chain: RO:0002215 RO:0002211 is_a: RO:0002500 ! causal agent in process [Typedef] @@ -1811,16 +1678,16 @@ 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 -holds_over_chain: capable_of RO:0002212 +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: example_of_usage "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -holds_over_chain: capable_of RO:0002213 +holds_over_chain: RO:0002215 RO:0002213 is_a: RO:0002596 ! capable of regulating [Typedef] @@ -1830,12 +1697,6 @@ def: "Inverse of 'causal agent in process'" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to -[Typedef] -id: RO:0002610 -name: correlated with -def: "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." [] -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string - [Typedef] id: RO:0002629 name: directly positively regulates @@ -1864,11 +1725,22 @@ property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regul is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates +[Typedef] +id: RO:0004028 +name: realized in response to stimulus +def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] +domain: BFO:0000017 ! realizable entity +range: BFO:0000040 ! material entity +holds_over_chain: RO:0009501 RO:0002233 +is_a: RO:0002410 ! causally related to +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-12-26T19:45:49Z + [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." [] -holds_over_chain: RO:0002327 has_part +holds_over_chain: RO:0002327 BFO:0000051 is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -1939,6 +1811,52 @@ is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z +[Typedef] +id: RO:0009501 +name: realized in response to +def: "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." [] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 +property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string +property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +holds_over_chain: BFO:0000054 RO:0002404 +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0010001 +name: generically depends on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string +property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string +property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string +property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string +property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0000052 RO:0000058 +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is carrier of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string +property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string +property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000031 ! generically dependent continuant +holds_over_chain: RO:0000059 RO:0000053 + [Typedef] id: RO:0011002 name: regulates activity of @@ -1970,31 +1888,21 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: example_of_usage "A diagnostic testing device utilizes a specimen." xsd:string +property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string -holds_over_chain: capable_of RO:0002233 +holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z -[Typedef] -id: RO:0017003 -name: positively correlated with -def: "A relation between entities in which one increases or decreases as the other does the same." [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 -property_value: IAO:0000118 "directly correlated with" xsd:string -is_reflexive: true -is_symmetric: true -is_a: RO:0002610 ! correlated with - [Typedef] id: RO:0019000 name: regulates characteristic def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process -range: PATO:0000001 ! quality +range: PATO:0000001 holds_over_chain: RO:0002211 RO:0019000 is_a: RO:0002410 ! causally related to @@ -2042,125 +1950,10 @@ id: VFBext:0000009 name: has driver def: "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements." [PMID:8223268, Wikipedia:GAL4/UAS_system] domain: CARO:0030002 ! expression pattern -is_a: expresses ! expresses +is_a: RO:0002292 ! expresses created_by: dos creation_date: 2018-09-26T07:49:10Z -[Typedef] -id: capable_of -name: capable of -name: capable_of -namespace: fly_anatomy.ontology -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 -xref: RO:0002215 -property_value: example_of_usage "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: example_of_usage "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -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 -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: capable_of_part_of ! capable_of_part_of - -[Typedef] -id: capable_of_part_of -name: capable of part of -name: capable_of_part_of -namespace: fly_anatomy.ontology -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." [] -xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: characteristic_of -name: characteristic of -name: characteristic_of -namespace: fly_anatomy.ontology -def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] -comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -xref: RO:0000052 -property_value: example_of_usage "this fragility is a characteristic of this vase" xsd:string -property_value: example_of_usage "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 -is_functional: true -is_a: RO:0002314 ! characteristic of part of -inverse_of: has_characteristic ! has_characteristic - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -xref: IAO:0000116 -is_metadata_tag: true - -[Typedef] -id: example_of_usage -name: example of usage -namespace: uberon -xref: IAO:0000112 -is_metadata_tag: true - -[Typedef] -id: expresses -name: expresses -namespace: fly_anatomy.ontology -def: "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -xref: RO:0002292 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: has_characteristic -name: has characteristic -name: has_characteristic -namespace: fly_anatomy.ontology -def: "Inverse of characteristic_of" [] -xref: RO:0000053 -property_value: editor_note "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: example_of_usage "this apple is bearer of this red color" xsd:string -property_value: example_of_usage "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant -is_inverse_functional: true - -[Typedef] -id: has_part -name: has part -name: has_part -namespace: quality -namespace: relationship -def: "a core relation that holds between a whole and its part" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000051 -xref: OBO_REL:has_part -property_value: editor_note "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: editor_note "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "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: example_of_usage "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: example_of_usage "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: example_of_usage "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: overlaps ! overlaps - [Typedef] id: http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 name: has_exemplar @@ -2174,59 +1967,3 @@ is_a: RO:0002350 ! member of id: http://xmlns.com/foaf/0.1/depicts name: depicts -[Typedef] -id: overlaps -name: overlaps -namespace: fly_anatomy.ontology -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: part_of part_of -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of -expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] - -[Typedef] -id: part_of -name: part of -name: part_of -namespace: quality -namespace: relationship -def: "a core relation that holds between a part and its whole" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000050 -xref: OBO_REL:part_of -property_value: editor_note "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: editor_note "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "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: example_of_usage "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: example_of_usage "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: example_of_usage "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -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 -property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI -is_transitive: true -is_a: overlaps ! overlaps -inverse_of: has_part ! has part - diff --git a/vfbext-full.owl b/vfbext-full.owl index 0e863f4..8848f2d 100644 --- a/vfbext-full.owl +++ b/vfbext-full.owl @@ -2,7 +2,6 @@ + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 15:08:2023 10:37 + 26:10:2023 13:58 VFB extension ontology - 2023-08-15 + 2023-10-26 @@ -48,24 +43,6 @@ - - - - - - - - - - - - - - - - - - @@ -74,14 +51,7 @@ - - IAO:0000112 - uberon - example_of_usage - true - example_of_usage - example of usage - + @@ -94,47 +64,14 @@ - 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 - - IAO:0000116 - uberon - editor_note - true - editor_note - editor note - + @@ -168,6 +105,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -186,27 +129,9 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - + - - - - - - - - - - - - - + @@ -216,12 +141,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -318,17 +237,19 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + - + - + + + @@ -396,188 +317,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -586,67 +325,27 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - + - + @@ -718,12 +417,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -742,12 +435,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -774,23 +461,9 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - has_obo_namespace - + @@ -800,12 +473,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -820,36 +487,12 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - @@ -871,7 +514,7 @@ We also have the outstanding issue of how to aim different definitions to differ @@ -879,24 +522,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - + @@ -921,18 +547,11 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - BFO:0000050 - OBO_REL:part_of - quality - relationship - part_of - part_of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -958,30 +577,48 @@ 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 - BFO:0000051 - OBO_REL:has_part - quality - relationship - has_part - has_part 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 + @@ -1002,7 +639,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1036,12 +673,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - @@ -1051,7 +682,17 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has_specified_input + has_specified_input + see is_input_of example_of_usage + The inverse property of is_specified_input_of + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot + has_specified_input @@ -1061,7 +702,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + is_specified_input_of + some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters is_specified_input_of @@ -1076,7 +722,15 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has_specified_output + has_specified_output + The inverse property of is_specified_output_of + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot + has_specified_output @@ -1086,7 +740,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + is_specified_output_of + is_specified_output_of + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + is_specified_output_of @@ -1095,21 +755,18 @@ A continuant cannot have an occurrent as part: use 'participates in'. + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective - - - - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. - objective_achieved_by - - - - @@ -1122,13 +779,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in - RO:0000052 - fly_anatomy.ontology - characteristic_of - characteristic_of Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of - characteristic_of @@ -1146,12 +798,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - RO:0000053 - fly_anatomy.ontology - has_characteristic - has_characteristic has characteristic - has_characteristic @@ -1178,6 +825,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + @@ -1189,15 +841,36 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + 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 + @@ -1564,14 +1237,9 @@ Examples include: the relationship between two channels collected simultaneously 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) - RO:0002131 - fly_anatomy.ontology - overlaps - overlaps - overlaps overlaps @@ -1655,9 +1323,6 @@ Examples include: the relationship between two channels collected simultaneously Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false - RO:0002211 - gene_ontology - regulates @@ -1677,9 +1342,6 @@ Examples include: the relationship between two channels collected simultaneously negatively regulates (process to process) - RO:0002212 - gene_ontology - negatively_regulates @@ -1704,9 +1366,6 @@ Examples include: the relationship between two channels collected simultaneously positively regulates (process to process) - RO:0002213 - gene_ontology - positively_regulates @@ -1729,13 +1388,8 @@ Examples include: the relationship between two channels collected simultaneously 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:0002215 - fly_anatomy.ontology - capable_of - capable_of capable of - capable_of @@ -1752,12 +1406,7 @@ Examples include: the relationship between two channels collected simultaneously 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. has function in - RO:0002216 - fly_anatomy.ontology - capable_of_part_of - capable_of_part_of capable of part of - capable_of_part_of @@ -1851,11 +1500,6 @@ Examples include: the relationship between two channels collected simultaneously y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - RO:0002292 - fly_anatomy.ontology - expresses - expresses - expresses expresses @@ -2745,16 +2389,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - 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 - - - - @@ -2791,6 +2425,24 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. + + 2017-12-26T19:45:49Z + realized in response to stimulus + + + + @@ -2909,6 +2561,79 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. + An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) + 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. + + + + + triggered by process + realized in response to + https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit + + + + + triggered by process + + + + + + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + @@ -2960,27 +2685,13 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material - - - - - - - A relation between entities in which one increases or decreases as the other does the same. - directly correlated with - - positively correlated with - - - - @@ -3124,43 +2835,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - 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]) - - - - - - @@ -3174,76 +2851,9 @@ For example, A and B may be gene products and binding of B by A positively regul - continuant - Continuant 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. - 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 - - - - 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] - - @@ -3280,65 +2890,10 @@ For example, A and B may be gene products and binding of B by A positively regul - 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 - 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]) - 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] 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 - - - - 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] - - @@ -3485,10 +3040,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CARO:0000000 Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. @@ -3503,6 +3054,60 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + + Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. + connected anatomical structure + + + + + + + + + Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle. + Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome. + portion of organism substance + CARO:0000004 + Note - CARO explicitly declares organisms substances to be part of (some) organism. + organism substance + + + + @@ -3573,1286 +3178,758 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - An anatomical structure consisting of one or more cells. - - 2018-09-28T14:20:19Z - cellular anatomical structure + + + Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. + CARO:0000012 + MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + +MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. + multicellular organism - + - - - Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. - Important for alignment with Darwin Core class "Organism". - biological entity + + + + + + + + + An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CL:0000000 + GO:0005623 + CARO:0000013 + deprecate and replace with CL or GO term? + cell - + - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. - expression pattern + + + + + + + + + + + + + Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher. + cell component + CARO:0000014 + This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class. + cell part - + - - - Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. - CARO:0000003 - UBERON:0000061 - fly_anatomy.ontology - FBbt:00007001 - - - anatomical structure + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism. + CARO:0000032 + + organism subdivision - - - - Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. - CARO:MAH - FBC:DOS - - + - - - CARO:0000006 - UBERON:0000465 - fly_anatomy.ontology - FBbt:00007016 - - - material anatomical entity + + + + + + + + 0 + + + + + 0 + + + + + + + + + + + An anatomical structure that has no cells or cell parts as a part. + CARO:0000040 + Example. Insect cuticle, eggshell, hair. + acellular anatomical structure - + - - - Anatomical structure that has multiple cells as parts. - - 2010-11-02T02:25:04Z - UBERON:0010000 - fly_anatomy.ontology - FBbt:00100313 - multicellular structure + + + + + + A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. + CARO:0000042 + + MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids? + + extraembryonic structure - - - - Anatomical structure that has multiple cells as parts. - FBC:DOS - - + - - + + + - + - - + + + + + + + + + + 2 + - - - - - - - - - Anatomical entity which is part_of Drosophila melanogaster. - FBbt_root:00000000 - UBERON:0001062 - fly_anatomy.ontology - Drosophila - FBbt:10000000 - - - - anatomical entity + + A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. + multi-cell-component structure + CARO:0001000 + + Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain. + multi-cell-part structure - - - - Anatomical entity which is part_of Drosophila melanogaster. - CARO:MAH - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GO:0005554 - molecular function - molecular_function - GO:0003674 - - - - - - - Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. - molecular_function - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GOC:pdt - - - + - - - - - Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. - Wikipedia:Enzyme - enzyme activity - molecular_function - GO:0003824 - - - - - - - - catalytic activity + + + + + + + + + + + + + + + + + + + + + Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. + + 10.7.2011 + + gross anatomical part - - - - Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. - GOC:vw - ISBN:0198506732 - - - - - enzyme activity - GOC:dph - GOC:tb - - + - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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. - https://github.com/geneontology/go-ontology/issues/24968 - jl - 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 + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + Melissa Haendel + 9/18/11 + organism or virus or viroid + organism - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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 - - + - - + + + + - - true + + - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - Reactome:R-HSA-6788855 - Reactome:R-HSA-6788867 - phosphokinase activity - molecular_function - GO:0016301 - - - - - - Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. - kinase activity + An anatomical structure that has more than one cell as a part. + djs93 + Sun Feb 27 10:53:00 GMT 2011 + CARO:0010000 + + multicellular anatomical structure - - - - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - ISBN:0198506732 - - - - - Reactome:R-HSA-6788855 - FN3KRP phosphorylates PsiAm, RibAm - - - - - Reactome:R-HSA-6788867 - FN3K phosphorylates ketosamines - - - - - - - - - Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. - EC:2.-.-.- - Reactome:R-HSA-1483089 - Reactome:R-HSA-1483186 - Reactome:R-HSA-5668414 - Reactome:R-HSA-8868783 - molecular_function - GO:0016740 - - - - - - - - - - - transferase activity + + + + + + + + - - - Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. - ISBN:0198506732 - - - - - Reactome:R-HSA-1483089 - PE is converted to PS by PTDSS2 - - - - - Reactome:R-HSA-1483186 - PC is converted to PS by PTDSS1 - - - - - Reactome:R-HSA-5668414 - TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK - - - - - Reactome:R-HSA-8868783 - TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 + + + + There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS - + - - - Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). - EC:2.7.-.- - molecular_function - GO:0016772 - - Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. - transferase activity, transferring phosphorus-containing groups + + + + An individual member of a clade of cellular organisms. + + 7.16.2011 + CARO:0010004 + 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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + cellular organism - - - - Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). - GOC:jl - ISBN:0198506732 - - + - + - - - - - - - - - - - + + + + + + + + + 2 + + + - 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 - - - - - - - - GC_ID:1 - ncbi_taxonomy - all - NCBITaxon:1 - root - - - - - all - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:1206794 - Ecdysozoa - - - - - - - - - GC_ID:1 - ncbi_taxonomy - biota - NCBITaxon:131567 - cellular organisms - - - - - biota - - - - - - - - - - - GC_ID:1 - PMID:10874751 - PMID:11557979 - ncbi_taxonomy - NCBITaxon:197562 - Pancrustacea + + + + + + + + + + + + + + Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. + CARO:0000054 + + disconnected anatomical group - + - - - - GC_ID:1 - PMID:11557979 - PMID:9727836 - mandibulates - ncbi_taxonomy - NCBITaxon:197563 - Mandibulata + + + + An anatomical structure consisting of one or more cells. + + 2018-09-28T14:20:19Z + cellular anatomical structure - - - - mandibulates - - - - - - - - - - - GC_ID:1 - PMID:23020233 - PMID:30257078 - eucaryotes - eukaryotes - ncbi_taxonomy - Eucarya - Eucaryotae - Eukarya - Eukaryotae - eukaryotes - NCBITaxon:2759 - Eukaryota + + + + + + + + - - - eucaryotes - - - - - - eukaryotes - - - - - - Eucarya - - - - - - Eucaryotae - - - - - - Eukarya - - - - - - Eukaryotae - - - - - - eukaryotes - + + + + With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32341 - Sophophora - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32346 - melanogaster group - - - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32351 - melanogaster subgroup + + + Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. + Important for alignment with Darwin Core class "Organism". + biological entity - + - - - - GC_ID:1 - ncbi_taxonomy - Fungi/Metazoa group - opisthokonts - NCBITaxon:33154 - Opisthokonta + + + + + + + + + The mereological sum of all cells in a single organism in which expression of some specified gene occurs. + expression pattern - - - - Fungi/Metazoa group - - - - - - opisthokonts - - - + - - - - GC_ID:1 - metazoans - multicellular animals - ncbi_taxonomy - Animalia - animals - NCBITaxon:33208 - Metazoa + + + Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. + CARO:0000003 + UBERON:0000061 + fly_anatomy.ontology + FBbt:00007001 + + + anatomical structure - - - metazoans - - - - - - multicellular animals - - - - - - Animalia - - - - - - animals - + + + Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. + https://orcid.org/0000-0001-9114-8737 + https://orcid.org/0000-0002-7073-9172 - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33213 - Bilateria - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33317 - Protostomia - - - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33340 - Neoptera + + + CARO:0000006 + UBERON:0000465 + fly_anatomy.ontology + FBbt:00007016 + + + material anatomical entity - + - - - - GC_ID:1 - ncbi_taxonomy - Holometabola - NCBITaxon:33392 - Endopterygota + + + Anatomical structure that has multiple cells as parts. + + 2010-11-02T02:25:04Z + UBERON:0010000 + fly_anatomy.ontology + FBbt:00100313 + multicellular structure - - - Holometabola - + + + Anatomical structure that has multiple cells as parts. + https://orcid.org/0000-0002-7073-9172 - + - - - - NCBITaxon:43732 - GC_ID:1 - ncbi_taxonomy - Asilomorpha - NCBITaxon:43733 - Muscomorpha + + + + + + + + + + + + + + + + + + + + + Anatomical entity which is part_of Drosophila melanogaster. + FBbt_root:00000000 + UBERON:0001062 + fly_anatomy.ontology + Drosophila + FBbt:10000000 + + + + anatomical entity - - - Asilomorpha - + + + Anatomical entity which is part_of Drosophila melanogaster. + https://orcid.org/0000-0001-9114-8737 - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43738 - Schizophora - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43741 - Acalyptratae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43746 - Ephydroidea - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43845 - Drosophilinae - - - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:46877 - Drosophilini - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:480117 - Cyclorrhapha + + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:480118 - Eremoneura + + + + + true + + - + - - - - GC_ID:1 - true insects - ncbi_taxonomy - insects - NCBITaxon:50557 - Insecta - - - - - true insects - - - - - - insects - - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:6072 - Eumetazoa - + - + - - - - GC_ID:1 - arthropods - ncbi_taxonomy - arthropods - NCBITaxon:6656 - Arthropoda - - - - - arthropods - - - - - - arthropods - - + - + - - - - GC_ID:1 - insects - ncbi_taxonomy - Atelocerata - Tracheata - Uniramia - hexapods - NCBITaxon:6960 - Hexapoda + + + + + + + + + + + + + + + + + + + + + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A process that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + planned process - - - - insects - - - - - - Atelocerata - - - - - - Tracheata - - - - - - Uniramia - - - - - - hexapods - - - + - - - - GC_ID:1 - flies - ncbi_taxonomy - flies - NCBITaxon:7147 - Diptera + + + + + + + + + + + + + + + + + + + specimen role + liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. + + a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen. + parasite example +- when parasite in people we study people, people are subjects and parasites are specimen +- when parasite extracted, they become subject in the following study +specimen can later be subject. + GROUP: Role Branch + OBI + + specimen role - - - - flies - - - - - - flies - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:7203 - Brachycera + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specimen collection process + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + + A planned process with the objective of collecting a specimen. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. + Philly2013: The specimen_role for the specimen is created during the specimen collection process. + label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/ + Bjoern Peters + specimen collection + 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession + 6/9/09: used at workshop + specimen collection process - + - - - - GC_ID:1 - pomace flies - ncbi_taxonomy - NCBITaxon:7214 - Drosophilidae + + + specimen collection objective + The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. + + A objective specification to obtain a material entity for potential use as an input during an investigation. + Bjoern Peters + Bjoern Peters + specimen collection objective - - - - pomace flies - - - + - - - - NCBITaxon:7326 - GC_ID:1 - Drosophila - fruit flies - fruit fly - ncbi_taxonomy - NCBITaxon:7215 - Drosophila <flies,genus> + + + + + + + + + + + + + + collection of specimens + Blood cells collected from multiple donors over the course of a study. + + A material entity that has two or more specimens as its parts. + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Person: Chris Stoeckert, Jie Zheng + OBIB, OBI + Biobank + collection of specimens - - - - Drosophila - - - - - - fruit flies - - - - - - fruit fly - - - + - - - - NCBITaxon:2267365 - GC_ID:1 - fruit fly - ncbi_taxonomy - Sophophora melanogaster - NCBITaxon:7227 - Drosophila melanogaster + + + + + + + + + + + + + + + + + + + + specimen + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + + A material entity that has the specimen role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch + + specimen - - - - fruit fly - - - - - - Sophophora melanogaster - - - + - - - - GC_ID:1 - Pterygota - winged insects - ncbi_taxonomy - NCBITaxon:7496 - Pterygota <insects> - - - - - Pterygota - - - - - - winged insects - - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:85512 - Dicondylia - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:88770 - Panarthropoda - + - + - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - 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 dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. - PATOC:GVG - + - + - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - quality - PATO:0000125 - - - - For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. - mass - - - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - PATOC:GVG - + - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 - Wikipedia:Physical_property - relational physical quality - quality - PATO:0001018 - - 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 a continuant. - PATO:0001237 - PATO:0001238 - snap:Quality - monadic quality of a continuant - multiply inhering quality of a physical entity - 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 - + - + - + - - Anatomical entity that has mass. - - - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FBbt:00007016 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - UBERON:0000465 - - - material anatomical entity - - - - Anatomical entity that has mass. - http://orcid.org/0000-0001-9114-8737 - - + - - - 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. - - - AAO:0010841 - AEO:0000000 - BILA:0000000 - BIRNLEX:6 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FMA:62955 - HAO:0000000 - MA:0000001 - NCIT:C12219 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - WBbt:0000100 - XAO:0000000 - ZFA:0100000 - UBERON:0001062 - - - anatomical entity - - - - - 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. - FMA:62955 - http://orcid.org/0000-0001-9114-8737 - - - - - UMLS:C1515976 - ncithesaurus:Anatomic_Structure_System_or_Substance - + @@ -4941,115 +4018,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - metadata complete - 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 - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - ready for release - - 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 - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - - 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 - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - - 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 - - - - - - - - - - - - - - - - - - - - Should belong in BFO, but lives in caro for now. - - - - - @@ -5113,17 +4060,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - + + + + + + @@ -5142,10 +4084,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + @@ -5190,15 +4132,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -5208,15 +4150,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -5282,10 +4224,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5293,9 +4234,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5325,10 +4267,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5336,9 +4277,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5368,10 +4310,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5379,9 +4320,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5411,10 +4353,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5422,9 +4363,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5889,9 +4831,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -5900,9 +4842,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -5934,9 +4876,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -5945,9 +4887,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -5979,9 +4921,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -5990,9 +4932,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6024,9 +4966,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6035,9 +4977,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6069,9 +5011,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6080,9 +5022,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6114,7 +5056,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6125,7 +5067,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6142,7 +5084,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6152,7 +5094,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6170,7 +5112,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6181,7 +5123,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6198,7 +5140,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6208,7 +5150,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6225,7 +5167,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6236,7 +5178,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6269,9 +5211,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6280,9 +5222,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6313,9 +5255,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6324,9 +5266,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6357,9 +5299,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6368,9 +5310,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6401,9 +5343,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6412,9 +5354,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6446,8 +5388,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -6457,8 +5399,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -6485,5 +5427,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/vfbext-non-classified.json b/vfbext-non-classified.json index 7d03b4b..ab40d71 100644 --- a/vfbext-non-classified.json +++ b/vfbext-non-classified.json @@ -13,167 +13,24 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "15:08:2023 10:37" + "val" : "26:10:2023 13:58" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-15" + "val" : "2023-10-26" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-08-15/vfbext-non-classified.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-10-26/vfbext-non-classified.json" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000078", - "lbl" : "curation status specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "curation status specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bill Bug" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000266" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000001", - "lbl" : "entity", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "entity" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "Entity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Julius Caesar" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Verdi’s Requiem" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the Second World War" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "your body mass index" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "Continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", @@ -192,62 +49,7 @@ "definition" : { "val" : "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])" }, - "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "ic" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "IndependentContinuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a chair" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a heart" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a leg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a molecule" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a spatial region" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an atom" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an orchestra." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an organism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the bottom right portion of a human torso" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the interior of your mouth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(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] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", @@ -320,18 +122,13 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a part and its whole" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - }, { - "val" : "OBO_REL:part_of" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is part of" @@ -380,15 +177,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "relationship" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" @@ -405,18 +193,13 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a whole and its part" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - }, { - "val" : "OBO_REL:has_part" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has part" @@ -444,15 +227,64 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "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" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realized in" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease is realized in this disease course" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "relationship" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is realized in this shattering" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is realized in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is realized by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "realized_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "[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])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "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" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realizes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease course realizes this disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation realizes this investigator role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this shattering realizes this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "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])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { @@ -477,7 +309,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } @@ -515,1383 +347,727 @@ "comments" : [ "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure." ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000006", - "lbl" : "material anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000003", + "lbl" : "connected anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical entity that has mass." + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." }, + "comments" : [ "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development." ], "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000007", - "lbl" : "immaterial anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000004", + "lbl" : "organism substance", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that has no mass." + "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." }, - "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] + "comments" : [ "Note - CARO explicitly declares organisms substances to be part of (some) organism." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "portion of organism substance" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle." + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0020003", - "lbl" : "cellular anatomical structure", + "id" : "http://purl.obolibrary.org/obo/CARO_0000006", + "lbl" : "material anatomical entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure consisting of one or more cells." + "val" : "An anatomical entity that has mass." }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-09-28T14:20:19Z" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0030000", - "lbl" : "biological entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000007", + "lbl" : "immaterial anatomical entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." + "val" : "Anatomical entity that has no mass." }, - "comments" : [ "Important for alignment with Darwin Core class \"Organism\"." ] + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0030002", - "lbl" : "expression pattern", + "id" : "http://purl.obolibrary.org/obo/CARO_0000012", + "lbl" : "multicellular organism", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." - } + "val" : "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." + }, + "comments" : [ "MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. \n\nMH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities." ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_00007001", - "lbl" : "anatomical structure", + "id" : "http://purl.obolibrary.org/obo/CARO_0000013", + "lbl" : "cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.", - "xrefs" : [ "CARO:MAH", "FBC:DOS" ] + "val" : "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." }, - "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], + "comments" : [ "deprecate and replace with CL or GO term?" ], "xrefs" : [ { - "val" : "CARO:0000003" + "val" : "CL:0000000" }, { - "val" : "UBERON:0000061" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "val" : "GO:0005623" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_00007016", - "lbl" : "material anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000014", + "lbl" : "cell part", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], - "xrefs" : [ { - "val" : "CARO:0000006" - }, { - "val" : "UBERON:0000465" - } ], + "definition" : { + "val" : "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." + }, + "comments" : [ "This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "cell component" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_00100313", - "lbl" : "multicellular structure", + "id" : "http://purl.obolibrary.org/obo/CARO_0000032", + "lbl" : "organism subdivision", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that has multiple cells as parts.", - "xrefs" : [ "FBC:DOS" ] + "val" : "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." }, - "xrefs" : [ { - "val" : "UBERON:0010000" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2010-11-02T02:25:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_10000000", - "lbl" : "anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000040", + "lbl" : "acellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity which is part_of Drosophila melanogaster.", - "xrefs" : [ "CARO:MAH" ] + "val" : "An anatomical structure that has no cells or cell parts as a part." }, - "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#EmbDevSlim", "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Drosophila" - } ], - "xrefs" : [ { - "val" : "UBERON:0001062" - } ], + "comments" : [ "Example. Insect cuticle, eggshell, hair." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000042", + "lbl" : "extraembryonic structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." + }, + "comments" : [ "MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: \"Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.\". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?\n" ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#plus" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001000", + "lbl" : "multi-cell-part structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." + }, + "comments" : [ "Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain." ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "FBbt_root:00000000" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-cell-component structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003674", - "lbl" : "molecular_function", + "id" : "http://purl.obolibrary.org/obo/CARO_0001008", + "lbl" : "gross anatomical part", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", - "xrefs" : [ "GOC:pdt" ] + "val" : "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecular function" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#plus" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005554" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "10.7.2011" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003824", - "lbl" : "catalytic activity", + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "lbl" : "organism", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.", - "xrefs" : [ "GOC:vw", "ISBN:0198506732" ] + "val" : "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "enzyme activity", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - } ], - "xrefs" : [ { - "val" : "Wikipedia:Enzyme" + "val" : "organism or virus or viroid" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Melissa Haendel" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "9/18/11" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0008150", - "lbl" : "biological_process", + "id" : "http://purl.obolibrary.org/obo/CARO_0010000", + "lbl" : "multicellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.", - "xrefs" : [ "GOC:pdt" ] + "val" : "An anatomical structure that has more than one cell as a part." }, - "comments" : [ "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." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "biological process" - }, { - "pred" : "hasExactSynonym", - "val" : "physiological process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single organism process" + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "djs93" }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism process" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Biological_process" - } ], + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Sun Feb 27 10:53:00 GMT 2011" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0010004", + "lbl" : "cellular organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An individual member of a clade of cellular organisms." + }, + "comments" : [ "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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. " ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/24968" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "7.16.2011" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0020000", + "lbl" : "disconnected anatomical group", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0020003", + "lbl" : "cellular anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure consisting of one or more cells." + }, + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" + "val" : "2018-09-28T14:20:19Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016301", - "lbl" : "kinase activity", + "id" : "http://purl.obolibrary.org/obo/CARO_0030000", + "lbl" : "biological entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", - "xrefs" : [ "ISBN:0198506732" ] + "val" : "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." }, - "comments" : [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "phosphokinase activity" - } ], + "comments" : [ "Important for alignment with Darwin Core class \"Organism\"." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0030002", + "lbl" : "expression pattern", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/FBbt_00007001", + "lbl" : "anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.", + "xrefs" : [ "https://orcid.org/0000-0001-9114-8737", "https://orcid.org/0000-0002-7073-9172" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], "xrefs" : [ { - "val" : "Reactome:R-HSA-6788855" + "val" : "CARO:0000003" }, { - "val" : "Reactome:R-HSA-6788867" + "val" : "UBERON:0000061" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "val" : "fly_anatomy.ontology" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016740", - "lbl" : "transferase activity", + "id" : "http://purl.obolibrary.org/obo/FBbt_00007016", + "lbl" : "material anatomical entity", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], "xrefs" : [ { - "val" : "EC:2.-.-.-" - }, { - "val" : "Reactome:R-HSA-1483089" - }, { - "val" : "Reactome:R-HSA-1483186" - }, { - "val" : "Reactome:R-HSA-5668414" + "val" : "CARO:0000006" }, { - "val" : "Reactome:R-HSA-8868783" + "val" : "UBERON:0000465" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "val" : "fly_anatomy.ontology" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016772", - "lbl" : "transferase activity, transferring phosphorus-containing groups", + "id" : "http://purl.obolibrary.org/obo/FBbt_00100313", + "lbl" : "multicellular structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).", - "xrefs" : [ "GOC:jl", "ISBN:0198506732" ] + "val" : "Anatomical structure that has multiple cells as parts.", + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, - "comments" : [ "Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "xrefs" : [ { - "val" : "EC:2.7.-.-" + "val" : "UBERON:0010000" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2010-11-02T02:25:04Z" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" + "val" : "fly_anatomy.ontology" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000112", - "lbl" : "example of usage", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/FBbt_10000000", + "lbl" : "anatomical entity", + "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Anatomical entity which is part_of Drosophila melanogaster.", + "xrefs" : [ "https://orcid.org/0000-0001-9114-8737" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#EmbDevSlim", "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "Drosophila" + } ], "xrefs" : [ { - "val" : "IAO:0000112" + "val" : "UBERON:0001062" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "FBbt_root:00000000" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "example_of_usage" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "fly_anatomy.ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "lbl" : "definition", - "type" : "PROPERTY", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "lbl" : "planned process", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." + "val" : "A process that realizes a plan which is the concretization of a plan specification." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Injecting mice with a vaccine in order to test its efficacy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " + "val" : "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" + "val" : "Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "branch derived" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "6/11/9: Edited at workshop. Used to include: is initiated by an agent" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000112", + "lbl" : "specimen role", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "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." + "val" : "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" + "val" : "specimen role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "blood taken from animal: animal continues in study, whereas blood has role specimen.\nsomething taken from study subject, leaves the study and becomes the specimen." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "parasite example\n- when parasite in people we study people, people are subjects and parasites are specimen\n- when parasite extracted, they become subject in the following study\nspecimen can later be subject." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP: Role Branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obi-ontology/obi/issues/1013" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "lbl" : "has_specified_input", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + "val" : "The inverse property of is_specified_input_of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "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.\"" - }, - "basicPropertyValues" : [ { + "val" : "has_specified_input" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" + "val" : "has_specified_input" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "see is_input_of example_of_usage" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Larry Hunter" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Coutot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000295", + "lbl" : "is_specified_input_of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. 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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." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "monadic quality of a continuant" - }, { - "pred" : "hasExactSynonym", - "val" : "multiply inhering quality of a physical entity" - }, { - "pred" : "hasExactSynonym", - "val" : "multiply inhering quality of a physical entity " - }, { - "pred" : "hasExactSynonym", - "val" : "quality of a continuant" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "specimen" }, { - "pred" : "hasExactSynonym", - "val" : "quality of a single physical entity" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." }, { - "pred" : "hasExactSynonym", - "val" : "quality of an object" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { - "pred" : "hasExactSynonym", - "val" : "quality of continuant" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." }, { - "pred" : "hasNarrowSynonym", - "val" : "monadic quality of an object" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: James Malone" }, { - "pred" : "hasNarrowSynonym", - "val" : "monadic quality of continuant" - } ], - "xrefs" : [ { - "val" : "snap:Quality" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Philippe Rocca-Serra" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP: OBI Biomaterial Branch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obi-ontology/obi/issues/1013" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic_of", + "lbl" : "characteristic of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." }, "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], - "xrefs" : [ { - "val" : "RO:0000052" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "inheres in" @@ -1907,25 +1083,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "characteristic_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has_characteristic", + "lbl" : "has characteristic", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of characteristic_of" }, - "xrefs" : [ { - "val" : "RO:0000053" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "bearer of" @@ -1947,12 +1114,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_characteristic" } ] } }, { @@ -2007,10 +1168,42 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "lbl" : "is concretized as", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "lbl" : "concretizes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000079", "lbl" : "function of", @@ -2379,9 +1572,6 @@ "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002131" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -2391,12 +1581,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "overlaps" } ] } }, { @@ -2453,9 +1637,6 @@ "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002211" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-7476-6306" @@ -2480,9 +1661,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "false" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "gene_ontology" } ] } }, { @@ -2494,9 +1672,6 @@ "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002212" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" @@ -2509,9 +1684,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "gene_ontology" } ] } }, { @@ -2523,9 +1695,6 @@ "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002213" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" @@ -2538,23 +1707,17 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "gene_ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable_of", + "lbl" : "capable of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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. " }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002215" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" @@ -2576,37 +1739,22 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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)\"." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002216", - "lbl" : "capable_of_part_of", + "lbl" : "capable of part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, - "xrefs" : [ { - "val" : "RO:0002216" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function in" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of_part_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -2705,21 +1853,12 @@ "definition" : { "val" : "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." }, - "xrefs" : [ { - "val" : "RO:0002292" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "expresses" } ] } }, { @@ -3687,19 +2826,6 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002610", - "lbl" : "correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Groups both positive and negative correlation" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "lbl" : "directly positively regulates", @@ -3746,6 +2872,22 @@ "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004031", "lbl" : "enables subfunction", @@ -3838,52 +2980,145 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:53:22Z" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" + "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004046", - "lbl" : "causally upstream of or within, negative effect", + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "lbl" : "generically depends on", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "g-depends on" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Genetic information generically depend on molecules of DNA." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The novel *War and Peace* generically depends on this copy of the novel." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:55:05Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The pattern shared by chess boards generically depends on any chess board." }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The score of a symphony g-depends on a copy of the score." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This pdf file generically depends on this server." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "[072-ISO]" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004047", - "lbl" : "causally upstream of or within, positive effect", + "id" : "http://purl.obolibrary.org/obo/RO_0010002", + "lbl" : "is carrier of", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Molecules of DNA are carriers of genetic information." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : 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"http://purl.obolibrary.org/obo/PATO_0001241" + "sub" : "http://purl.obolibrary.org/obo/OBI_0000659", + "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100051" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001241", + "sub" : "http://purl.obolibrary.org/obo/OBI_0000684", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" + "obj" : "http://purl.obolibrary.org/obo/IAO_0000005" }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "sub" : "http://purl.obolibrary.org/obo/OBI_0002076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "sub" : "http://purl.obolibrary.org/obo/OBI_0100051", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "sub" : "http://purl.obolibrary.org/obo/SO_0000110", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", "pred" : "is_a", @@ -4560,14 +3625,6 @@ "sub" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", "pred" : "is_a", "obj" : "http://xmlns.com/foaf/0.1/image" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000428", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "subPropertyOf", @@ -5024,6 +4081,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002630", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004028", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002410" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004031", "pred" : "subPropertyOf", @@ -5060,6 +4121,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004047", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0009501", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002410" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011002", "pred" : "subPropertyOf", @@ -5076,10 +4141,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0017003", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002610" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0019000", "pred" : "subPropertyOf", @@ -5112,6 +4173,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000055" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000062", "pred" : "inverseOf", @@ -5124,6 +4189,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000056", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000058", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000059" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000079", "pred" : "inverseOf", @@ -5204,14 +4273,35 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002559", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002566" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0010001", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0010002" } ], "logicalDefinitionAxioms" : [ { + "definedClassId" : "http://purl.obolibrary.org/obo/CARO_0000003", + "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0002266" + }, { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0010000" + } ] + }, { "definedClassId" : "http://purl.obolibrary.org/obo/CARO_0000006", "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000125" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CARO_0010000", + "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001993" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/FBbt_10000000", "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], @@ -5219,6 +4309,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0000659", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000417", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000684" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0100051", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000112" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004", "genusIds" : [ "http://purl.obolibrary.org/obo/FBbt_00100313" ], @@ -5258,6 +4362,14 @@ "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000055", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000062", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -5274,6 +4386,14 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000059", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ] @@ -5356,6 +4476,22 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0011002", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -5392,6 +4528,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000055", "http://purl.obolibrary.org/obo/RO_0000052" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -5401,9 +4540,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002584", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000054", "http://purl.obolibrary.org/obo/RO_0002404" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/RO_0000058" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -5536,6 +4684,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] } ] } ] } \ No newline at end of file diff --git a/vfbext-non-classified.obo b/vfbext-non-classified.obo index cea7d22..7213ba3 100644 --- a/vfbext-non-classified.obo +++ b/vfbext-non-classified.obo @@ -1,24 +1,10 @@ format-version: 1.2 -data-version: vfbext/releases/2023-08-15/vfbext-non-classified.owl -date: 15:08:2023 10:37 -subsetdef: attribute_slim "" +data-version: vfbext/releases/2023-10-26/vfbext-non-classified.owl +date: 26:10:2023 13:58 subsetdef: clone "" -subsetdef: common_anatomy "" subsetdef: core "" subsetdef: cur "" subsetdef: EmbDevSlim "" -subsetdef: goslim_agr "" -subsetdef: goslim_candida "" -subsetdef: goslim_chembl "" -subsetdef: goslim_drosophila "" -subsetdef: goslim_flybase_ribbon "" -subsetdef: goslim_generic "" -subsetdef: goslim_metagenomics "" -subsetdef: goslim_mouse "" -subsetdef: goslim_pir "" -subsetdef: goslim_plant "" -subsetdef: goslim_pombe "" -subsetdef: goslim_yeast "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -26,96 +12,40 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: larval_OF "" subsetdef: neuron "" subsetdef: ns_part "" -subsetdef: prokaryote_subset "" -subsetdef: relational_slim "" +subsetdef: plus "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" -subsetdef: scalar_slim "" subsetdef: synaptic_neuropil "" subsetdef: tract "" -subsetdef: upper_level "" -synonymtypedef: blast_name "" -synonymtypedef: common_name "" -synonymtypedef: genbank_common_name "" -synonymtypedef: in_part "" -synonymtypedef: scientific_name "" -synonymtypedef: synonym "" remark: VFB extension ontology ontology: vfbext/vfbext-non-classified property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2023-08-15" xsd:string - -[Term] -id: BFO:0000001 -name: entity -property_value: BFO:0000179 "entity" xsd:string -property_value: BFO:0000180 "Entity" xsd:string -property_value: editor_note "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: editor_note "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: example_of_usage "Julius Caesar" xsd:string -property_value: example_of_usage "the Second World War" xsd:string -property_value: example_of_usage "Verdi’s Requiem" xsd:string -property_value: example_of_usage "your body mass index" xsd:string -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 +property_value: owl:versionInfo "2023-10-26" xsd:string [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." [] -is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: part_of BFO:0000002 {all_only="true"} ! continuant -property_value: BFO:0000179 "continuant" xsd:string -property_value: BFO:0000180 "Continuant" xsd:string -property_value: editor_note "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: editor_note "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 +relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: part_of BFO:0000003 {all_only="true"} ! occurrent +relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent [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." [] -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"} +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])" [] comment: 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 disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant -property_value: BFO:0000179 "ic" xsd:string -property_value: BFO:0000180 "IndependentContinuant" xsd:string -property_value: example_of_usage "a chair" xsd:string -property_value: example_of_usage "a heart" xsd:string -property_value: example_of_usage "a leg" xsd:string -property_value: example_of_usage "a molecule" xsd:string -property_value: example_of_usage "a spatial region" xsd:string -property_value: example_of_usage "an atom" xsd:string -property_value: example_of_usage "an orchestra." xsd:string -property_value: example_of_usage "an organism" xsd:string -property_value: example_of_usage "the bottom right portion of a human torso" xsd:string -property_value: example_of_usage "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 +relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant [Term] id: BFO:0000015 @@ -136,13 +66,13 @@ name: realizable entity def: "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." [] is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality -relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity +relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant -relationship: part_of BFO:0000019 {all_only="true"} ! quality +relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 @@ -151,7 +81,7 @@ def: "b is a specifically dependent continuant = Def. b is a continuant & there comment: 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 disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant [Term] id: BFO:0000023 @@ -165,7 +95,7 @@ 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])" [] comment: 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. is_a: BFO:0000002 ! continuant -relationship: part_of BFO:0000031 {all_only="true"} ! generically dependent continuant +relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant [Term] id: BFO:0000034 @@ -191,6 +121,29 @@ def: "A part of a cellular organism that is either an immaterial entity or a mat comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. is_a: CARO:0030000 ! biological entity +[Term] +id: CARO:0000003 +name: connected anatomical structure +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [] +comment: Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. +subset: core +is_a: CARO:0000006 ! material anatomical entity +intersection_of: CARO:0000006 ! material anatomical entity +intersection_of: RO:0000053 PATO:0002266 ! has characteristic +intersection_of: RO:0000053 PATO:0010000 ! has characteristic +disjoint_from: CARO:0000004 ! organism substance +relationship: RO:0000053 PATO:0002266 ! has characteristic +relationship: RO:0000053 PATO:0010000 ! has characteristic + +[Term] +id: CARO:0000004 +name: organism substance +def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." [] +comment: Note - CARO explicitly declares organisms substances to be part of (some) organism. +synonym: "portion of organism substance" EXACT [] +is_a: CARO:0001008 ! gross anatomical part +property_value: IAO:0000112 "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle." xsd:string + [Term] id: CARO:0000006 name: material anatomical entity @@ -198,9 +151,9 @@ def: "An anatomical entity that has mass." [] subset: core is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity -intersection_of: has_characteristic PATO:0000125 ! mass +intersection_of: RO:0000053 PATO:0000125 ! has characteristic disjoint_from: CARO:0000007 ! immaterial anatomical entity -relationship: has_characteristic PATO:0000125 ! mass +relationship: RO:0000053 PATO:0000125 ! has characteristic [Term] id: CARO:0000007 @@ -210,6 +163,144 @@ subset: core is_a: BFO:0000141 ! immaterial entity is_a: CARO:0000000 ! anatomical entity +[Term] +id: CARO:0000012 +name: multicellular organism +def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] +comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. \n\nMH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. +is_a: CARO:0010004 ! cellular organism + +[Term] +id: CARO:0000013 +name: cell +def: "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [] +comment: deprecate and replace with CL or GO term? +xref: CL:0000000 +xref: GO:0005623 +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0020003 ! cellular anatomical structure +disjoint_from: CARO:0000014 ! cell part +disjoint_from: CARO:0000040 ! acellular anatomical structure +disjoint_from: CARO:0000042 ! extraembryonic structure +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure + +[Term] +id: CARO:0000014 +name: cell part +def: "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." [] +comment: This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class. +is_a: CARO:0000003 ! connected anatomical structure +disjoint_from: CARO:0000040 ! acellular anatomical structure +disjoint_from: CARO:0000042 ! extraembryonic structure +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 CARO:0000013 ! part of cell +property_value: IAO:0000118 "cell component" xsd:string + +[Term] +id: CARO:0000032 +name: organism subdivision +def: "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [] +subset: core +is_a: CARO:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." xsd:string + +[Term] +id: CARO:0000040 +name: acellular anatomical structure +def: "An anatomical structure that has no cells or cell parts as a part." [] +comment: Example. Insect cuticle, eggshell, hair. +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001008 ! gross anatomical part +intersection_of: CARO:0000003 ! connected anatomical structure +intersection_of: RO:0002180 CARO:0000013 {cardinality="0"} ! has component cell +intersection_of: RO:0002180 CARO:0000014 {cardinality="0"} ! has component cell part +disjoint_from: CARO:0000042 ! extraembryonic structure +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure + +[Term] +id: CARO:0000042 +name: extraembryonic structure +def: "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." [] +comment: MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?\n +subset: plus +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001008 ! gross anatomical part +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure + +[Term] +id: CARO:0001000 +name: multi-cell-part structure +def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [] +comment: Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain. +subset: core +is_a: CARO:0001008 ! gross anatomical part +disjoint_from: CARO:0010000 ! multicellular anatomical structure +property_value: IAO:0000118 "multi-cell-component structure" xsd:string + +[Term] +id: CARO:0001008 +name: gross anatomical part +def: "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " [] +subset: plus +is_a: CARO:0000006 ! material anatomical entity +union_of: CARO:0000004 ! organism substance +union_of: CARO:0000032 ! organism subdivision +union_of: CARO:0000040 ! acellular anatomical structure +union_of: CARO:0000042 ! extraembryonic structure +union_of: CARO:0001000 ! multi-cell-part structure +union_of: CARO:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 CARO:0000012 ! part of multicellular organism +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.7.2011" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 + +[Term] +id: CARO:0001010 +name: organism +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +synonym: "organism or virus or viroid" EXACT [] +is_a: BFO:0000040 ! material entity +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000117 "Melissa Haendel" xsd:string + +[Term] +id: CARO:0010000 +name: multicellular anatomical structure +def: "An anatomical structure that has more than one cell as a part." [] +subset: core +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001008 ! gross anatomical part +intersection_of: CARO:0000003 {comment="There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS"} ! connected anatomical structure +intersection_of: RO:0000053 PATO:0001993 {comment="There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS"} ! has characteristic +relationship: RO:0000053 PATO:0001993 ! has characteristic +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Sun Feb 27 10:53:00 GMT 2011" xsd:string +property_value: IAO:0000117 "djs93" xsd:string + +[Term] +id: CARO:0010004 +name: cellular organism +def: "An individual member of a clade of cellular organisms." [] +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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001010 ! organism +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 + +[Term] +id: CARO:0020000 +name: disconnected anatomical group +def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [] +subset: core +is_a: CARO:0000006 ! material anatomical entity +intersection_of: CARO:0000006 ! material anatomical entity +intersection_of: RO:0000053 PATO:0010001 ! has characteristic +intersection_of: RO:0002180 CARO:0000003 {minCardinality="2"} ! has component connected anatomical structure +relationship: RO:0000053 PATO:0010001 ! has characteristic +relationship: RO:0002180 CARO:0000003 ! has component connected anatomical structure + [Term] id: CARO:0020003 name: cellular anatomical structure @@ -230,12 +321,13 @@ id: CARO:0030002 name: expression pattern def: "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." [] is_a: CARO:0020003 ! cellular anatomical structure +relationship: BFO:0000051 CARO:0000013 ! has part cell [Term] id: FBbt:00007001 name: anatomical structure namespace: fly_anatomy.ontology -def: "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome." [CARO:MAH, FBC:DOS] +def: "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome." [https://orcid.org/0000-0001-9114-8737, https://orcid.org/0000-0002-7073-9172] subset: cur subset: larval_OF xref: CARO:0000003 @@ -256,10 +348,10 @@ is_a: FBbt:10000000 ! anatomical entity id: FBbt:00100313 name: multicellular structure namespace: fly_anatomy.ontology -def: "Anatomical structure that has multiple cells as parts." [FBC:DOS] +def: "Anatomical structure that has multiple cells as parts." [https://orcid.org/0000-0002-7073-9172] xref: UBERON:0010000 is_a: FBbt:00007001 ! anatomical structure -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 property_value: http://purl.org/dc/terms/date "2010-11-02T02:25:04Z" xsd:dateTime [Term] @@ -267,555 +359,122 @@ id: FBbt:10000000 name: anatomical entity namespace: fly_anatomy.ontology alt_id: FBbt_root:00000000 -def: "Anatomical entity which is part_of Drosophila melanogaster." [CARO:MAH] +def: "Anatomical entity which is part_of Drosophila melanogaster." [https://orcid.org/0000-0001-9114-8737] subset: cur subset: EmbDevSlim subset: larval_OF synonym: "Drosophila" RELATED [] xref: UBERON:0001062 -is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity -intersection_of: part_of NCBITaxon:7227 ! Drosophila melanogaster -disjoint_from: PATO:0000001 ! quality -relationship: part_of NCBITaxon:7227 ! Drosophila melanogaster - -[Term] -id: GO:0003674 -name: molecular_function -namespace: molecular_function -alt_id: GO:0005554 -def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] -comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. -subset: goslim_candida -subset: goslim_chembl -subset: goslim_metagenomics -subset: goslim_pir -subset: goslim_plant -subset: goslim_yeast -synonym: "molecular function" EXACT [] - -[Term] -id: GO:0003824 -name: catalytic activity -namespace: molecular_function -def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732] -subset: goslim_agr -subset: goslim_chembl -subset: goslim_flybase_ribbon -subset: goslim_generic -subset: goslim_metagenomics -subset: goslim_pir -subset: goslim_plant -synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] -xref: Wikipedia:Enzyme -is_a: GO:0003674 ! molecular_function +intersection_of: BFO:0000050 NCBITaxon:7227 ! part of +disjoint_from: PATO:0000001 [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 is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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_candida -subset: goslim_chembl -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: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl -creation_date: 2012-09-19T15:05:24Z +disjoint_from: OBI:0000011 ! planned process [Term] id: GO:0016301 -name: kinase activity -namespace: molecular_function -def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] -comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_metagenomics -subset: goslim_plant -subset: goslim_yeast -synonym: "phosphokinase activity" EXACT [] -xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm" -xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines" -is_a: GO:0003674 ! molecular_function -is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups - -[Term] -id: GO:0016740 -name: transferase activity -namespace: molecular_function -def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732] -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_generic -subset: goslim_metagenomics -subset: goslim_mouse -subset: goslim_pir -subset: goslim_plant -subset: goslim_yeast -subset: prokaryote_subset -xref: EC:2.-.-.- -xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2" -xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1" -xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK" -xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248" -is_a: GO:0003824 ! catalytic activity - -[Term] -id: GO:0016772 -name: transferase activity, transferring phosphorus-containing groups -namespace: molecular_function -def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] -comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. -subset: goslim_chembl -xref: EC:2.7.-.- -is_a: GO:0016740 ! transferase activity [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." [] -property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string -property_value: IAO:0000111 "curation status specification" xsd:string +id: OBI:0000011 +name: planned process +def: "A process that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string +property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000119 "branch derived" xsd:string +property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string +property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + +[Term] +id: OBI:0000112 +name: specimen role +def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] +is_a: BFO:0000023 ! role +property_value: IAO:0000111 "specimen role" xsd:string +property_value: IAO:0000112 "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role." xsd:string +property_value: IAO:0000116 "blood taken from animal: animal continues in study, whereas blood has role specimen.\nsomething taken from study subject, leaves the study and becomes the specimen." xsd:string +property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string +property_value: IAO:0000116 "parasite example\n- when parasite in people we study people, people are subjects and parasites are specimen\n- when parasite extracted, they become subject in the following study\nspecimen can later be subject." xsd:string +property_value: IAO:0000117 "GROUP: Role Branch" xsd:string +property_value: IAO:0000119 "OBI" xsd:string +property_value: IAO:0000233 https://github.com/obi-ontology/obi/issues/1013 + +[Term] +id: OBI:0000659 +name: specimen collection process +def: "A planned process with the objective of collecting a specimen." [] +is_a: OBI:0000011 ! planned process +intersection_of: OBI:0000011 ! planned process +intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective +relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity +relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen +property_value: IAO:0000111 "specimen collection process" xsd:string +property_value: IAO:0000112 "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "label changed to 'specimen collection process' on 10/27/2014, details see tracker:\nhttp://sourceforge.net/p/obi/obi-terms/716/" xsd:string +property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string +property_value: IAO:0000116 "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role." xsd:string +property_value: IAO:0000116 "Philly2013: The specimen_role for the specimen is created during the specimen collection process." xsd:string +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000118 "specimen collection" xsd:string +property_value: IAO:0000232 "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession" xsd:string +property_value: IAO:0000232 "6/9/09: used at workshop" xsd:string + +[Term] +id: OBI:0000684 +name: specimen collection objective +def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] +is_a: IAO:0000005 +property_value: IAO:0000111 "specimen collection objective" xsd:string +property_value: IAO:0000112 "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000119 "Bjoern Peters" xsd:string + +[Term] +id: OBI:0002076 +name: collection of specimens +def: "A material entity that has two or more specimens as its parts." [] +is_a: BFO:0000040 ! material entity +intersection_of: BFO:0000040 ! material entity +intersection_of: RO:0002351 OBI:0100051 {all_only="true"} ! has member specimen +property_value: http://purl.org/dc/elements/1.1/source "Biobank" xsd:string +property_value: IAO:0000111 "collection of specimens" xsd:string +property_value: IAO:0000112 "Blood cells collected from multiple donors over the course of a study." xsd:string property_value: IAO:0000114 IAO:0000125 -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: NCBITaxon:1 -name: root -namespace: ncbi_taxonomy -synonym: "all" RELATED synonym [] -xref: GC_ID:1 - -[Term] -id: NCBITaxon:1206794 -name: Ecdysozoa -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33317 ! Protostomia -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:131567 -name: cellular organisms -namespace: ncbi_taxonomy -synonym: "biota" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1 ! root - -[Term] -id: NCBITaxon:197562 -name: Pancrustacea -namespace: ncbi_taxonomy -xref: GC_ID:1 -xref: PMID:10874751 -xref: PMID:11557979 -is_a: NCBITaxon:197563 ! Mandibulata -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:197563 -name: Mandibulata -namespace: ncbi_taxonomy -synonym: "mandibulates" EXACT common_name [] -xref: GC_ID:1 -xref: PMID:11557979 -xref: PMID:9727836 -is_a: NCBITaxon:6656 ! Arthropoda -property_value: has_rank NCBITaxon:clade - -[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 -xref: PMID:30257078 -is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom - -[Term] -id: NCBITaxon:32341 -name: Sophophora -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7215 ! Drosophila -property_value: has_rank NCBITaxon:subgenus - -[Term] -id: NCBITaxon:32346 -name: melanogaster group -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:32341 ! Sophophora -property_value: has_rank NCBITaxon:species_group - -[Term] -id: NCBITaxon:32351 -name: melanogaster subgroup -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:32346 ! melanogaster group -property_value: has_rank NCBITaxon:species_subgroup - -[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: has_rank NCBITaxon:clade - -[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 - -[Term] -id: NCBITaxon:33213 -name: Bilateria -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:33317 -name: Protostomia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:33340 -name: Neoptera -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7496 ! Pterygota -property_value: has_rank NCBITaxon:infraclass - -[Term] -id: NCBITaxon:33392 -name: Endopterygota -namespace: ncbi_taxonomy -synonym: "Holometabola" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:33340 ! Neoptera -property_value: has_rank NCBITaxon:cohort - -[Term] -id: NCBITaxon:43733 -name: Muscomorpha -namespace: ncbi_taxonomy -alt_id: NCBITaxon:43732 -synonym: "Asilomorpha" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:7203 ! Brachycera -property_value: has_rank NCBITaxon:infraorder - -[Term] -id: NCBITaxon:43738 -name: Schizophora -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:480117 ! Cyclorrhapha - -[Term] -id: NCBITaxon:43741 -name: Acalyptratae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43738 ! Schizophora - -[Term] -id: NCBITaxon:43746 -name: Ephydroidea -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43741 ! Acalyptratae -property_value: has_rank NCBITaxon:superfamily - -[Term] -id: NCBITaxon:43845 -name: Drosophilinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7214 ! Drosophilidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:46877 -name: Drosophilini -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43845 ! Drosophilinae -property_value: has_rank NCBITaxon:tribe - -[Term] -id: NCBITaxon:480117 -name: Cyclorrhapha -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:480118 ! Eremoneura -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:480118 -name: Eremoneura -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43733 ! Muscomorpha -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:50557 -name: Insecta -namespace: ncbi_taxonomy -synonym: "insects" RELATED blast_name [] -synonym: "true insects" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:6960 ! Hexapoda -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:6072 -name: Eumetazoa -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade +property_value: IAO:0000116 "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/" xsd:string +property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string +property_value: IAO:0000119 "OBIB, OBI" xsd:string [Term] -id: NCBITaxon:6656 -name: Arthropoda -namespace: ncbi_taxonomy -synonym: "arthropods" EXACT genbank_common_name [] -synonym: "arthropods" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:88770 ! Panarthropoda -property_value: has_rank NCBITaxon:phylum - -[Term] -id: NCBITaxon:6960 -name: Hexapoda -namespace: ncbi_taxonomy -synonym: "Atelocerata" RELATED in_part [] -synonym: "hexapods" RELATED blast_name [] -synonym: "insects" EXACT genbank_common_name [] -synonym: "Tracheata" RELATED in_part [] -synonym: "Uniramia" RELATED in_part [] -xref: GC_ID:1 -is_a: NCBITaxon:197562 ! Pancrustacea -property_value: has_rank NCBITaxon:subphylum - -[Term] -id: NCBITaxon:7147 -name: Diptera -namespace: ncbi_taxonomy -synonym: "flies" EXACT genbank_common_name [] -synonym: "flies" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:33392 ! Endopterygota -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:7203 -name: Brachycera -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7147 ! Diptera -property_value: has_rank NCBITaxon:suborder - -[Term] -id: NCBITaxon:7214 -name: Drosophilidae -namespace: ncbi_taxonomy -synonym: "pomace flies" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:43746 ! Ephydroidea -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:7215 -name: Drosophila -namespace: ncbi_taxonomy -alt_id: NCBITaxon:7326 -synonym: "Drosophila" EXACT scientific_name [] -synonym: "fruit flies" EXACT genbank_common_name [] -synonym: "fruit fly" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:46877 ! Drosophilini -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:7227 -name: Drosophila melanogaster -namespace: ncbi_taxonomy -alt_id: NCBITaxon:2267365 -synonym: "fruit fly" EXACT genbank_common_name [] -synonym: "Sophophora melanogaster" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:32351 ! melanogaster subgroup -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:7496 -name: Pterygota -namespace: ncbi_taxonomy -synonym: "Pterygota" EXACT scientific_name [] -synonym: "winged insects" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:85512 ! Dicondylia -property_value: has_rank NCBITaxon:subclass - -[Term] -id: NCBITaxon:85512 -name: Dicondylia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:50557 ! Insecta -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:88770 -name: Panarthropoda -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1206794 ! Ecdysozoa -property_value: has_rank NCBITaxon:clade - -[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] -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 [] -is_a: BFO:0000020 ! specifically dependent continuant - -[Term] -id: PATO:0000125 -name: mass -namespace: quality -def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [PATOC:GVG] -comment: For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. -subset: attribute_slim -subset: relational_slim -subset: scalar_slim -is_a: PATO:0001018 ! physical quality - -[Term] -id: PATO:0001018 -name: physical quality -namespace: quality -alt_id: PATO:0002079 -def: "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] -subset: attribute_slim -synonym: "relational physical quality" EXACT [] -xref: Wikipedia:Physical_property -is_a: PATO:0001241 ! physical object quality - -[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: "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 - -[Term] -id: UBERON:0000465 -name: material anatomical entity -def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] -subset: common_anatomy -subset: upper_level -xref: AAO:0010264 -xref: AEO:0000006 -xref: BILA:0000006 -xref: CARO:0000006 -xref: EHDAA2:0003006 -xref: FBbt:00007016 -xref: FMA:67165 -xref: HAO:0000006 -xref: TAO:0001836 -xref: TGMA:0001826 -xref: VHOG:0001721 +id: OBI:0100051 +name: specimen +def: "A material entity that has the specimen role." [] +is_a: BFO:0000040 ! material entity +intersection_of: BFO:0000040 ! material entity +intersection_of: RO:0000087 OBI:0000112 ! has role specimen role +property_value: IAO:0000111 "specimen" xsd:string +property_value: IAO:0000112 "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string +property_value: IAO:0000117 "PERSON: James Malone" xsd:string +property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string +property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string +property_value: IAO:0000233 https://github.com/obi-ontology/obi/issues/1013 + +[Term] +id: SO:0000110 is_a: BFO:0000040 ! material entity -is_a: UBERON:0001062 ! anatomical entity -property_value: RO:0002175 NCBITaxon:33090 -property_value: RO:0002175 NCBITaxon:4751 - -[Term] -id: UBERON:0001062 -name: anatomical entity -def: "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." [FMA:62955, http://orcid.org/0000-0001-9114-8737] -subset: common_anatomy -subset: upper_level -xref: AAO:0010841 -xref: AEO:0000000 -xref: BILA:0000000 -xref: BIRNLEX:6 -xref: CARO:0000000 -xref: EHDAA2:0002229 -xref: FBbt:10000000 -xref: FMA:62955 -xref: HAO:0000000 -xref: MA:0000001 -xref: NCIT:C12219 -xref: TAO:0100000 -xref: TGMA:0001822 -xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} -xref: WBbt:0000100 -xref: XAO:0000000 -xref: ZFA:0100000 -is_a: BFO:0000004 ! independent continuant -property_value: RO:0002175 NCBITaxon:33090 -property_value: RO:0002175 NCBITaxon:4751 [Term] id: VFB:10000005 @@ -827,7 +486,7 @@ id: VFBext:0000004 name: expression pattern fragment comment: A multicellular structure that is part of an expression pattern. intersection_of: FBbt:00100313 ! multicellular structure -intersection_of: part_of CARO:0030002 ! expression pattern +intersection_of: BFO:0000050 CARO:0030002 ! part of expression pattern created_by: dos creation_date: 2018-03-04T10:55:59Z @@ -856,19 +515,99 @@ id: VFBext:0000014 name: channel is_a: http://xmlns.com/foaf/0.1/image +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: 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 +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI +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" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: BFO:0000054 +name: realized in +comment: 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 +property_value: IAO:0000111 "realized in" xsd:string +property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string +property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string +property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string +property_value: IAO:0000118 "is realized by" xsd:string +property_value: IAO:0000118 "realized_in" xsd:string +property_value: IAO:0000600 "[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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +inverse_of: BFO:0000055 ! realizes + +[Typedef] +id: BFO:0000055 +name: realizes +comment: 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 +property_value: IAO:0000111 "realizes" xsd:string +property_value: IAO:0000112 "this disease course realizes this disease" xsd:string +property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string +property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string +property_value: IAO:0000600 "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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +domain: BFO:0000015 ! process +range: BFO:0000017 ! realizable entity + [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: editor_note "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: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/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 domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000062 +holds_over_chain: BFO:0000050 BFO:0000062 is_transitive: true is_a: RO:0002086 ! ends after inverse_of: BFO:0000063 ! precedes @@ -881,7 +620,7 @@ subset: ro-eco property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000063 +holds_over_chain: BFO:0000050 BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to @@ -889,44 +628,102 @@ is_a: RO:0002222 ! temporally related to id: OBI:0000293 name: has_specified_input def: "The inverse property of is_specified_input_of" [] +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl is_a: RO:0000057 ! has participant [Typedef] id: OBI:0000295 name: is_specified_input_of def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "is_specified_input_of" xsd:string +property_value: IAO:0000112 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl is_a: RO:0000057 ! has participant [Typedef] id: OBI:0000312 name: is_specified_output_of def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] +property_value: IAO:0000111 "achieves_planned_objective" xsd:string +property_value: IAO:0000112 "A cell sorting process achieves the objective specification 'material separation objective'" xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "BP, AR, PPPB branch" xsd:string +property_value: IAO:0000119 "PPPB branch derived" xsd:string +property_value: IAO:0000232 "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" xsd:string [Typedef] -id: OBI:0000833 -name: objective_achieved_by -def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] +id: RO:0000052 +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: RO:0002314 ! characteristic of part of +inverse_of: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000053 +name: has characteristic +def: "Inverse of characteristic_of" [] +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: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant +is_inverse_functional: true [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: example_of_usage "this blood clot participates in this blood coagulation" xsd:string -property_value: example_of_usage "this input material (or this output material) participates in this process" xsd:string -property_value: example_of_usage "this investigator participates in this investigation" xsd:string 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 domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent @@ -936,28 +733,47 @@ inverse_of: RO:0000057 ! has participant 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: editor_note "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: example_of_usage "this blood coagulation has participant this blood clot" xsd:string -property_value: example_of_usage "this investigation has participant this investigator" xsd:string -property_value: example_of_usage "this process has participant this input material (or this output material)" xsd:string -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/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 domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant -holds_over_chain: has_part RO:0000057 +holds_over_chain: BFO:0000051 RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant [Typedef] id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function [Typedef] @@ -965,11 +781,11 @@ 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" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: example_of_usage "this red color is a quality of this apple" xsd:string +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 -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of inverse_of: RO:0000086 ! has quality [Typedef] @@ -977,44 +793,44 @@ id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this investigator role is a role of this person" xsd:string +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role [Typedef] id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic [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: editor_note "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: example_of_usage "this apple has quality this red color" xsd:string +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 range: BFO:0000019 ! quality -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000091 @@ -1022,7 +838,7 @@ name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic inverse_of: RO:0000092 ! disposition of [Typedef] @@ -1031,7 +847,7 @@ name: disposition of def: "inverse of has disposition" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. subset: RO:0002259 -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of [Typedef] id: RO:0002013 @@ -1157,40 +973,55 @@ property_value: IAO:0000118 "meets" xsd:string 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: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: RO:0001900 RO:0001901 +holds_over_chain: BFO:0000050 BFO:0000050 +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} +holds_over_chain: BFO:0000051 RO:0002131 +is_symmetric: true +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: editor_note "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: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: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002206 name: expressed in def: "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" [] -property_value: example_of_usage "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string +property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant -range: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 is_a: RO:0002330 ! genomically related to -inverse_of: expresses ! expresses -transitive_over: part_of ! part_of +inverse_of: RO:0002292 ! expresses +transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002211 name: regulates -namespace: gene_ontology def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002211 property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -1210,12 +1041,10 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively regulates -namespace: gene_ontology def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002212 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string @@ -1227,12 +1056,10 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -namespace: gene_ontology def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002213 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -1243,6 +1070,33 @@ 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 https://orcid.org/0000-0002-6601-2165 +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 +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of + +[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 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + [Typedef] id: RO:0002222 name: temporally related to @@ -1277,7 +1131,7 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: example_of_usage "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: 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: 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 @@ -1288,11 +1142,19 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: example_of_usage "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: 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: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002292 +name: expresses +def: "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002330 ! genomically related to + [Typedef] id: RO:0002304 name: causally upstream of, positive effect @@ -1322,15 +1184,15 @@ is_a: RO:0004046 ! causally upstream of or within, negative effect id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: characteristic_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002323 @@ -1345,7 +1207,7 @@ id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string @@ -1354,9 +1216,9 @@ 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: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI -is_a: capable_of ! capable_of +is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by -transitive_over: has_part ! has part +transitive_over: BFO:0000051 ! has part transitive_over: RO:0002017 ! has component activity [Typedef] @@ -1372,7 +1234,7 @@ 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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -1392,10 +1254,10 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI -holds_over_chain: RO:0002327 part_of +holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002333 @@ -1439,12 +1301,12 @@ is_a: RO:0002334 ! regulated by id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: example_of_usage "An organism that is a member of a population of organisms" xsd:string +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: RO:0001900 RO:0001901 -is_a: part_of ! part_of +is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] @@ -1453,7 +1315,7 @@ 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: RO:0001900 RO:0001901 -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002352 @@ -1519,7 +1381,7 @@ transitive_over: RO:0002630 ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 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 @@ -1548,7 +1410,7 @@ id: RO:0002418 name: causally upstream of or within def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true @@ -1599,7 +1461,7 @@ is_a: RO:0002428 ! involved in regulation of 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: editor_note "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -1613,8 +1475,8 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 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: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI @@ -1637,7 +1499,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 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 is_a: RO:0002436 ! molecularly interacts with @@ -1718,7 +1580,7 @@ property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 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 @@ -1779,9 +1641,9 @@ is_a: RO:0002412 ! immediately causally upstream of 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: example_of_usage "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: has_part capable_of +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 @@ -1789,7 +1651,7 @@ is_a: RO:0002595 ! causal relation between material entity and a process 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: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity @@ -1800,9 +1662,9 @@ is_a: RO:0002410 ! causally related to 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: example_of_usage "pyrethroid -> growth" xsd:string +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -holds_over_chain: capable_of RO:0002211 +holds_over_chain: RO:0002215 RO:0002211 is_a: RO:0002500 ! causal agent in process [Typedef] @@ -1810,16 +1672,16 @@ 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 -holds_over_chain: capable_of RO:0002212 +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: example_of_usage "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -holds_over_chain: capable_of RO:0002213 +holds_over_chain: RO:0002215 RO:0002213 is_a: RO:0002596 ! capable of regulating [Typedef] @@ -1829,12 +1691,6 @@ def: "Inverse of 'causal agent in process'" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to -[Typedef] -id: RO:0002610 -name: correlated with -def: "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." [] -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string - [Typedef] id: RO:0002629 name: directly positively regulates @@ -1863,11 +1719,22 @@ property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regul is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates +[Typedef] +id: RO:0004028 +name: realized in response to stimulus +def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] +domain: BFO:0000017 ! realizable entity +range: BFO:0000040 ! material entity +holds_over_chain: RO:0009501 RO:0002233 +is_a: RO:0002410 ! causally related to +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-12-26T19:45:49Z + [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." [] -holds_over_chain: RO:0002327 has_part +holds_over_chain: RO:0002327 BFO:0000051 is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -1938,6 +1805,52 @@ is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z +[Typedef] +id: RO:0009501 +name: realized in response to +def: "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." [] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 +property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string +property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +holds_over_chain: BFO:0000054 RO:0002404 +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0010001 +name: generically depends on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string +property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string +property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string +property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string +property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0000052 RO:0000058 +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is carrier of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string +property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string +property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000031 ! generically dependent continuant +holds_over_chain: RO:0000059 RO:0000053 + [Typedef] id: RO:0011002 name: regulates activity of @@ -1969,31 +1882,21 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: example_of_usage "A diagnostic testing device utilizes a specimen." xsd:string +property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string -holds_over_chain: capable_of RO:0002233 +holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z -[Typedef] -id: RO:0017003 -name: positively correlated with -def: "A relation between entities in which one increases or decreases as the other does the same." [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 -property_value: IAO:0000118 "directly correlated with" xsd:string -is_reflexive: true -is_symmetric: true -is_a: RO:0002610 ! correlated with - [Typedef] id: RO:0019000 name: regulates characteristic def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process -range: PATO:0000001 ! quality +range: PATO:0000001 holds_over_chain: RO:0002211 RO:0019000 is_a: RO:0002410 ! causally related to @@ -2041,125 +1944,10 @@ id: VFBext:0000009 name: has driver def: "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements." [PMID:8223268, Wikipedia:GAL4/UAS_system] domain: CARO:0030002 ! expression pattern -is_a: expresses ! expresses +is_a: RO:0002292 ! expresses created_by: dos creation_date: 2018-09-26T07:49:10Z -[Typedef] -id: capable_of -name: capable of -name: capable_of -namespace: fly_anatomy.ontology -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 -xref: RO:0002215 -property_value: example_of_usage "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: example_of_usage "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -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 -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: capable_of_part_of ! capable_of_part_of - -[Typedef] -id: capable_of_part_of -name: capable of part of -name: capable_of_part_of -namespace: fly_anatomy.ontology -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." [] -xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: characteristic_of -name: characteristic of -name: characteristic_of -namespace: fly_anatomy.ontology -def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] -comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -xref: RO:0000052 -property_value: example_of_usage "this fragility is a characteristic of this vase" xsd:string -property_value: example_of_usage "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 -is_functional: true -is_a: RO:0002314 ! characteristic of part of -inverse_of: has_characteristic ! has_characteristic - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -xref: IAO:0000116 -is_metadata_tag: true - -[Typedef] -id: example_of_usage -name: example of usage -namespace: uberon -xref: IAO:0000112 -is_metadata_tag: true - -[Typedef] -id: expresses -name: expresses -namespace: fly_anatomy.ontology -def: "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -xref: RO:0002292 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: has_characteristic -name: has characteristic -name: has_characteristic -namespace: fly_anatomy.ontology -def: "Inverse of characteristic_of" [] -xref: RO:0000053 -property_value: editor_note "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: example_of_usage "this apple is bearer of this red color" xsd:string -property_value: example_of_usage "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant -is_inverse_functional: true - -[Typedef] -id: has_part -name: has part -name: has_part -namespace: quality -namespace: relationship -def: "a core relation that holds between a whole and its part" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000051 -xref: OBO_REL:has_part -property_value: editor_note "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: editor_note "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "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: example_of_usage "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: example_of_usage "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: example_of_usage "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: overlaps ! overlaps - [Typedef] id: http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 name: has_exemplar @@ -2173,59 +1961,3 @@ is_a: RO:0002350 ! member of id: http://xmlns.com/foaf/0.1/depicts name: depicts -[Typedef] -id: overlaps -name: overlaps -namespace: fly_anatomy.ontology -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: part_of part_of -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of -expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] - -[Typedef] -id: part_of -name: part of -name: part_of -namespace: quality -namespace: relationship -def: "a core relation that holds between a part and its whole" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000050 -xref: OBO_REL:part_of -property_value: editor_note "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: editor_note "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "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: example_of_usage "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: example_of_usage "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: example_of_usage "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -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 -property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI -is_transitive: true -is_a: overlaps ! overlaps -inverse_of: has_part ! has part - diff --git a/vfbext-non-classified.owl b/vfbext-non-classified.owl index f53661a..c5a3950 100644 --- a/vfbext-non-classified.owl +++ b/vfbext-non-classified.owl @@ -2,7 +2,6 @@ + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 15:08:2023 10:37 + 26:10:2023 13:58 VFB extension ontology - 2023-08-15 + 2023-10-26 @@ -48,24 +43,6 @@ - - - - - - - - - - - - - - - - - - @@ -74,14 +51,7 @@ - - IAO:0000112 - uberon - example_of_usage - true - example_of_usage - example of usage - + @@ -94,47 +64,14 @@ - 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 - - IAO:0000116 - uberon - editor_note - true - editor_note - editor note - + @@ -168,6 +105,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -186,27 +129,9 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - + - - - - - - - - - - - - - + @@ -216,12 +141,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -318,17 +237,19 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + - + - + + + @@ -396,188 +317,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -586,67 +325,27 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - + - + @@ -718,12 +417,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -742,12 +435,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -774,23 +461,9 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - has_obo_namespace - + @@ -800,12 +473,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -820,36 +487,12 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - @@ -871,7 +514,7 @@ We also have the outstanding issue of how to aim different definitions to differ @@ -879,24 +522,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - + @@ -921,18 +547,11 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - BFO:0000050 - OBO_REL:part_of - quality - relationship - part_of - part_of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -958,30 +577,48 @@ 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 - BFO:0000051 - OBO_REL:has_part - quality - relationship - has_part - has_part 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 + @@ -1002,7 +639,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1036,12 +673,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - @@ -1051,7 +682,17 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has_specified_input + has_specified_input + see is_input_of example_of_usage + The inverse property of is_specified_input_of + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot + has_specified_input @@ -1061,7 +702,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + is_specified_input_of + some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters is_specified_input_of @@ -1076,7 +722,15 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has_specified_output + has_specified_output + The inverse property of is_specified_output_of + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot + has_specified_output @@ -1086,7 +740,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + is_specified_output_of + is_specified_output_of + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + is_specified_output_of @@ -1095,21 +755,18 @@ A continuant cannot have an occurrent as part: use 'participates in'. + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective - - - - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. - objective_achieved_by - - - - @@ -1122,13 +779,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in - RO:0000052 - fly_anatomy.ontology - characteristic_of - characteristic_of Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of - characteristic_of @@ -1146,12 +798,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - RO:0000053 - fly_anatomy.ontology - has_characteristic - has_characteristic has characteristic - has_characteristic @@ -1178,6 +825,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + @@ -1189,15 +841,36 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + 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 + @@ -1564,14 +1237,9 @@ Examples include: the relationship between two channels collected simultaneously 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) - RO:0002131 - fly_anatomy.ontology - overlaps - overlaps - overlaps overlaps @@ -1655,9 +1323,6 @@ Examples include: the relationship between two channels collected simultaneously Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false - RO:0002211 - gene_ontology - regulates @@ -1677,9 +1342,6 @@ Examples include: the relationship between two channels collected simultaneously negatively regulates (process to process) - RO:0002212 - gene_ontology - negatively_regulates @@ -1704,9 +1366,6 @@ Examples include: the relationship between two channels collected simultaneously positively regulates (process to process) - RO:0002213 - gene_ontology - positively_regulates @@ -1729,13 +1388,8 @@ Examples include: the relationship between two channels collected simultaneously 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:0002215 - fly_anatomy.ontology - capable_of - capable_of capable of - capable_of @@ -1752,12 +1406,7 @@ Examples include: the relationship between two channels collected simultaneously 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. has function in - RO:0002216 - fly_anatomy.ontology - capable_of_part_of - capable_of_part_of capable of part of - capable_of_part_of @@ -1851,11 +1500,6 @@ Examples include: the relationship between two channels collected simultaneously y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - RO:0002292 - fly_anatomy.ontology - expresses - expresses - expresses expresses @@ -2745,16 +2389,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - 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 - - - - @@ -2791,6 +2425,24 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. + + 2017-12-26T19:45:49Z + realized in response to stimulus + + + + @@ -2909,6 +2561,79 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. + An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) + 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. + + + + + triggered by process + realized in response to + https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit + + + + + triggered by process + + + + + + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + @@ -2960,27 +2685,13 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material - - - - - - - A relation between entities in which one increases or decreases as the other does the same. - directly correlated with - - positively correlated with - - - - @@ -3124,43 +2835,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - 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]) - - - - - - @@ -3174,76 +2851,9 @@ For example, A and B may be gene products and binding of B by A positively regul - continuant - Continuant 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. - 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 - - - - 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] - - @@ -3280,65 +2890,10 @@ For example, A and B may be gene products and binding of B by A positively regul - 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 - 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]) - 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] 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 - - - - 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] - - @@ -3485,10 +3040,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CARO:0000000 Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. @@ -3503,6 +3054,60 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + + Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. + connected anatomical structure + + + + + + + + + Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle. + Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome. + portion of organism substance + CARO:0000004 + Note - CARO explicitly declares organisms substances to be part of (some) organism. + organism substance + + + + @@ -3573,1287 +3178,728 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - An anatomical structure consisting of one or more cells. - - 2018-09-28T14:20:19Z - cellular anatomical structure + + + Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. + CARO:0000012 + MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + +MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. + multicellular organism - + - - - Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. - Important for alignment with Darwin Core class "Organism". - biological entity + + + + + + + + + An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CL:0000000 + GO:0005623 + CARO:0000013 + deprecate and replace with CL or GO term? + cell - + - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. - expression pattern + + + + + + + + + + + + + Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher. + cell component + CARO:0000014 + This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class. + cell part - + - - - Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. - CARO:0000003 - UBERON:0000061 - fly_anatomy.ontology - FBbt:00007001 - - - anatomical structure + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism. + CARO:0000032 + + organism subdivision - - - - Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. - CARO:MAH - FBC:DOS - - + - - - CARO:0000006 - UBERON:0000465 - fly_anatomy.ontology - FBbt:00007016 - - - material anatomical entity + + + + + + + + 0 + + + + + 0 + + + + + + + + + + + An anatomical structure that has no cells or cell parts as a part. + CARO:0000040 + Example. Insect cuticle, eggshell, hair. + acellular anatomical structure - + - - - Anatomical structure that has multiple cells as parts. - - 2010-11-02T02:25:04Z - UBERON:0010000 - fly_anatomy.ontology - FBbt:00100313 - multicellular structure + + + + + + A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. + CARO:0000042 + + MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids? + + extraembryonic structure - - - - Anatomical structure that has multiple cells as parts. - FBC:DOS - - + - - + + + - + - - + + + + + + + + + + 2 + - - - - - - - - - Anatomical entity which is part_of Drosophila melanogaster. - FBbt_root:00000000 - UBERON:0001062 - fly_anatomy.ontology - Drosophila - FBbt:10000000 - - - - anatomical entity + + A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. + multi-cell-component structure + CARO:0001000 + + Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain. + multi-cell-part structure - - - - Anatomical entity which is part_of Drosophila melanogaster. - CARO:MAH - - + - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GO:0005554 - molecular function - molecular_function - GO:0003674 - - - - - - - Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. - molecular_function + + + + + + + + + + + + + + + + + + + + + Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. + + 10.7.2011 + + gross anatomical part - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GOC:pdt - - - - - - Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. - Wikipedia:Enzyme - enzyme activity - molecular_function - GO:0003824 - - - - - - - - catalytic activity - - - - - Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. - GOC:vw - ISBN:0198506732 - - - - - enzyme activity - GOC:dph - GOC:tb - - - + - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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. - https://github.com/geneontology/go-ontology/issues/24968 - jl - 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 + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + Melissa Haendel + 9/18/11 + organism or virus or viroid + organism - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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 - - + - - - + + + + - - true + + - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - Reactome:R-HSA-6788855 - Reactome:R-HSA-6788867 - phosphokinase activity - molecular_function - GO:0016301 - - - - - - Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. - kinase activity + An anatomical structure that has more than one cell as a part. + djs93 + Sun Feb 27 10:53:00 GMT 2011 + CARO:0010000 + + multicellular anatomical structure - - - - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - ISBN:0198506732 - - - - - Reactome:R-HSA-6788855 - FN3KRP phosphorylates PsiAm, RibAm - - - - - Reactome:R-HSA-6788867 - FN3K phosphorylates ketosamines - - - - - - - - - Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. - EC:2.-.-.- - Reactome:R-HSA-1483089 - Reactome:R-HSA-1483186 - Reactome:R-HSA-5668414 - Reactome:R-HSA-8868783 - molecular_function - GO:0016740 - - - - - - - - - - - transferase activity + + + + + + + + - - - Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. - ISBN:0198506732 - - - - - Reactome:R-HSA-1483089 - PE is converted to PS by PTDSS2 - - - - - Reactome:R-HSA-1483186 - PC is converted to PS by PTDSS1 - - - - - Reactome:R-HSA-5668414 - TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK - - - - - Reactome:R-HSA-8868783 - TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 + + + + There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS - + - - - Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). - EC:2.7.-.- - molecular_function - GO:0016772 - - Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. - transferase activity, transferring phosphorus-containing groups + + + + An individual member of a clade of cellular organisms. + + 7.16.2011 + CARO:0010004 + 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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + cellular organism - - - - Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). - GOC:jl - ISBN:0198506732 - - + - + - - - - - - - - - - - + + + + + + + + + 2 + + + - 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 - - - - - - - - GC_ID:1 - ncbi_taxonomy - all - NCBITaxon:1 - root - - - - - all - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:1206794 - Ecdysozoa - - - - - - - - - GC_ID:1 - ncbi_taxonomy - biota - NCBITaxon:131567 - cellular organisms - - - - - biota - - - - - - - - - - - GC_ID:1 - PMID:10874751 - PMID:11557979 - ncbi_taxonomy - NCBITaxon:197562 - Pancrustacea + + + + + + + + + + + + + + Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. + CARO:0000054 + + disconnected anatomical group - + - - - - GC_ID:1 - PMID:11557979 - PMID:9727836 - mandibulates - ncbi_taxonomy - NCBITaxon:197563 - Mandibulata + + + + An anatomical structure consisting of one or more cells. + + 2018-09-28T14:20:19Z + cellular anatomical structure - - - - mandibulates - - - - - - - - - - - GC_ID:1 - PMID:23020233 - PMID:30257078 - eucaryotes - eukaryotes - ncbi_taxonomy - Eucarya - Eucaryotae - Eukarya - Eukaryotae - eukaryotes - NCBITaxon:2759 - Eukaryota + + + + + + + + - - - eucaryotes - - - - - - eukaryotes - - - - - - Eucarya - - - - - - Eucaryotae - - - - - - Eukarya - - - - - - Eukaryotae - - - - - - eukaryotes - + + + + With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32341 - Sophophora - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32346 - melanogaster group - - - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32351 - melanogaster subgroup + + + Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. + Important for alignment with Darwin Core class "Organism". + biological entity - + - - - - GC_ID:1 - ncbi_taxonomy - Fungi/Metazoa group - opisthokonts - NCBITaxon:33154 - Opisthokonta + + + + + + + + + The mereological sum of all cells in a single organism in which expression of some specified gene occurs. + expression pattern - - - - Fungi/Metazoa group - - - - - - opisthokonts - - - + - - - - GC_ID:1 - metazoans - multicellular animals - ncbi_taxonomy - Animalia - animals - NCBITaxon:33208 - Metazoa + + + Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. + CARO:0000003 + UBERON:0000061 + fly_anatomy.ontology + FBbt:00007001 + + + anatomical structure - - - metazoans - - - - - - multicellular animals - - - - - - Animalia - - - - - - animals - + + + Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. + https://orcid.org/0000-0001-9114-8737 + https://orcid.org/0000-0002-7073-9172 - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33213 - Bilateria - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33317 - Protostomia - - - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33340 - Neoptera + + + CARO:0000006 + UBERON:0000465 + fly_anatomy.ontology + FBbt:00007016 + + + material anatomical entity - + - - - - GC_ID:1 - ncbi_taxonomy - Holometabola - NCBITaxon:33392 - Endopterygota + + + Anatomical structure that has multiple cells as parts. + + 2010-11-02T02:25:04Z + UBERON:0010000 + fly_anatomy.ontology + FBbt:00100313 + multicellular structure - - - Holometabola - + + + Anatomical structure that has multiple cells as parts. + https://orcid.org/0000-0002-7073-9172 - + - - - - NCBITaxon:43732 - GC_ID:1 - ncbi_taxonomy - Asilomorpha - NCBITaxon:43733 - Muscomorpha + + + + + + + + + + + + + + Anatomical entity which is part_of Drosophila melanogaster. + FBbt_root:00000000 + UBERON:0001062 + fly_anatomy.ontology + Drosophila + FBbt:10000000 + + + + anatomical entity - - - Asilomorpha - + + + Anatomical entity which is part_of Drosophila melanogaster. + https://orcid.org/0000-0001-9114-8737 - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43738 - Schizophora - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43741 - Acalyptratae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43746 - Ephydroidea - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43845 - Drosophilinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:46877 - Drosophilini - - - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:480117 - Cyclorrhapha - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:480118 - Eremoneura + + - + - - - - GC_ID:1 - true insects - ncbi_taxonomy - insects - NCBITaxon:50557 - Insecta + + + + + true + + - - - - true insects - - - - - - insects - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:6072 - Eumetazoa - + - + - - - - GC_ID:1 - arthropods - ncbi_taxonomy - arthropods - NCBITaxon:6656 - Arthropoda - - - - - arthropods - - - - - - arthropods - - + - + - - - - GC_ID:1 - insects - ncbi_taxonomy - Atelocerata - Tracheata - Uniramia - hexapods - NCBITaxon:6960 - Hexapoda - - - - - insects - - - - - - Atelocerata - - - - - - Tracheata - - - - - - Uniramia - - - - - - hexapods - - + - + - - - - GC_ID:1 - flies - ncbi_taxonomy - flies - NCBITaxon:7147 - Diptera + + + + + + + + + + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A process that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + planned process - - - - flies - - - - - - flies - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:7203 - Brachycera + + + + + + + + + + + + + + + + + + + specimen role + liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. + + a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen. + parasite example +- when parasite in people we study people, people are subjects and parasites are specimen +- when parasite extracted, they become subject in the following study +specimen can later be subject. + GROUP: Role Branch + OBI + + specimen role - + - - - - GC_ID:1 - pomace flies - ncbi_taxonomy - NCBITaxon:7214 - Drosophilidae + + + + + + + + + + + + + + + + + + + + + + + + + + specimen collection process + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + + A planned process with the objective of collecting a specimen. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. + Philly2013: The specimen_role for the specimen is created during the specimen collection process. + label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/ + Bjoern Peters + specimen collection + 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession + 6/9/09: used at workshop + specimen collection process - - - - pomace flies - - - + - - - - NCBITaxon:7326 - GC_ID:1 - Drosophila - fruit flies - fruit fly - ncbi_taxonomy - NCBITaxon:7215 - Drosophila <flies,genus> + + + specimen collection objective + The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. + + A objective specification to obtain a material entity for potential use as an input during an investigation. + Bjoern Peters + Bjoern Peters + specimen collection objective - - - - Drosophila - - - - - - fruit flies - - - - - - fruit fly - - - + - - - - NCBITaxon:2267365 - GC_ID:1 - fruit fly - ncbi_taxonomy - Sophophora melanogaster - NCBITaxon:7227 - Drosophila melanogaster - - - - - fruit fly - - - - - - Sophophora melanogaster - - + + + + + + + + + + + + + + collection of specimens + Blood cells collected from multiple donors over the course of a study. + + A material entity that has two or more specimens as its parts. + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Person: Chris Stoeckert, Jie Zheng + OBIB, OBI + Biobank + collection of specimens + - + - - - - GC_ID:1 - Pterygota - winged insects - ncbi_taxonomy - NCBITaxon:7496 - Pterygota <insects> + + + + + + + + + + + + + + specimen + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + + A material entity that has the specimen role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch + + specimen - - - - Pterygota - - - - - - winged insects - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:85512 - Dicondylia - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:88770 - Panarthropoda - + - + - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - 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 dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. - PATOC:GVG - + - + - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - quality - PATO:0000125 - - - - For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. - mass - - - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - PATOC:GVG - + - + - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 - Wikipedia:Physical_property - relational physical quality - quality - PATO:0001018 - - 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 a continuant. - PATO:0001237 - PATO:0001238 - snap:Quality - monadic quality of a continuant - multiply inhering quality of a physical entity - 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 - + + + - + - + - - Anatomical entity that has mass. - - - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FBbt:00007016 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - UBERON:0000465 - - - material anatomical entity - - - - Anatomical entity that has mass. - http://orcid.org/0000-0001-9114-8737 - - + - - - 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. - - - AAO:0010841 - AEO:0000000 - BILA:0000000 - BIRNLEX:6 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FMA:62955 - HAO:0000000 - MA:0000001 - NCIT:C12219 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - WBbt:0000100 - XAO:0000000 - ZFA:0100000 - UBERON:0001062 - - - anatomical entity - - - - - 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. - FMA:62955 - http://orcid.org/0000-0001-9114-8737 - - - - - UMLS:C1515976 - ncithesaurus:Anatomic_Structure_System_or_Substance - + @@ -4935,115 +3981,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - metadata complete - 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 - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - ready for release - - 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 - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - - 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 - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - - 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 - - - - - - - - - - - - - - - - - - - - Should belong in BFO, but lives in caro for now. - - - - - @@ -5107,17 +4023,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - + + + + + + @@ -5136,10 +4047,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + @@ -5184,15 +4095,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -5202,15 +4113,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -5276,10 +4187,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5287,9 +4197,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5319,10 +4230,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5330,9 +4240,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5362,10 +4273,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5373,9 +4283,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5405,10 +4316,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5416,9 +4326,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5883,9 +4794,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -5894,9 +4805,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -5928,9 +4839,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -5939,9 +4850,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -5973,9 +4884,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -5984,9 +4895,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6018,9 +4929,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6029,9 +4940,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6063,9 +4974,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6074,9 +4985,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6108,7 +5019,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6119,7 +5030,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6136,7 +5047,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6146,7 +5057,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6164,7 +5075,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6175,7 +5086,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6192,7 +5103,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6202,7 +5113,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6219,7 +5130,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6230,7 +5141,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6263,9 +5174,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6274,9 +5185,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6307,9 +5218,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6318,9 +5229,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6351,9 +5262,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6362,9 +5273,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6395,9 +5306,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6406,9 +5317,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6440,8 +5351,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -6451,8 +5362,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -6479,5 +5390,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/vfbext-simple.json b/vfbext-simple.json index 65f8638..8251311 100644 --- a/vfbext-simple.json +++ b/vfbext-simple.json @@ -13,30 +13,25 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "15:08:2023 10:37" + "val" : "26:10:2023 13:58" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-15" + "val" : "2023-10-26" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-08-15/vfbext-simple.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-10-26/vfbext-simple.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a part and its whole" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - }, { - "val" : "OBO_REL:part_of" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is part of" @@ -85,15 +80,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "relationship" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" @@ -115,28 +101,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "lbl" : "definition", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", @@ -145,21 +110,12 @@ "definition" : { "val" : "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." }, - "xrefs" : [ { - "val" : "RO:0002292" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "expresses" } ] } }, { diff --git a/vfbext-simple.obo b/vfbext-simple.obo index d8c251a..276cb9d 100644 --- a/vfbext-simple.obo +++ b/vfbext-simple.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2023-08-15/vfbext-simple.owl -date: 15:08:2023 10:37 +data-version: vfbext/releases/2023-10-26/vfbext-simple.owl +date: 26:10:2023 13:58 subsetdef: clone "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -15,7 +15,7 @@ ontology: vfbext/vfbext-simple property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2023-08-15" xsd:string +property_value: owl:versionInfo "2023-10-26" xsd:string [Term] id: VFB:10000005 @@ -50,6 +50,43 @@ creation_date: 2018-09-26T07:54:17Z id: VFBext:0000014 name: channel +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: 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 +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI +is_transitive: true + +[Typedef] +id: RO:0002292 +name: expresses +def: "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 + [Typedef] id: RO:0002350 name: member of @@ -59,7 +96,7 @@ 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: RO:0001900 RO:0001901 -is_a: part_of ! part_of +is_a: BFO:0000050 ! part of [Typedef] id: VFBext:0000001 @@ -87,19 +124,10 @@ creation_date: 2018-09-26T07:48:55Z id: VFBext:0000009 name: has driver def: "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements." [PMID:8223268, Wikipedia:GAL4/UAS_system] -is_a: expresses ! expresses +is_a: RO:0002292 ! expresses created_by: dos creation_date: 2018-09-26T07:49:10Z -[Typedef] -id: expresses -name: expresses -namespace: fly_anatomy.ontology -def: "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -xref: RO:0002292 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 - [Typedef] id: http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 name: has_exemplar @@ -113,38 +141,3 @@ is_a: RO:0002350 ! member of id: http://xmlns.com/foaf/0.1/depicts name: depicts -[Typedef] -id: part_of -name: part of -name: part_of -namespace: quality -namespace: relationship -def: "a core relation that holds between a part and its whole" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000050 -xref: OBO_REL:part_of -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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: 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 -property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI -is_transitive: true - diff --git a/vfbext-simple.owl b/vfbext-simple.owl index 1b7a3e1..81138d7 100644 --- a/vfbext-simple.owl +++ b/vfbext-simple.owl @@ -11,16 +11,15 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:vfb1="http://purl.obolibrary.org/obo/fbbt/vfb/" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 15:08:2023 10:37 + 26:10:2023 13:58 VFB extension ontology - 2023-08-15 + 2023-10-26 @@ -36,12 +35,6 @@ - - - - - - @@ -63,32 +56,6 @@ - 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 @@ -210,42 +177,12 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -276,12 +213,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -290,12 +221,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -322,18 +247,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - @@ -342,12 +255,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - + diff --git a/vfbext.json b/vfbext.json index 952e0a8..0df5373 100644 --- a/vfbext.json +++ b/vfbext.json @@ -13,167 +13,24 @@ "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#date", - "val" : "15:08:2023 10:37" + "val" : "26:10:2023 13:58" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "VFB extension ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-15" + "val" : "2023-10-26" } ], - "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-08-15/vfbext.json" + "version" : "http://purl.obolibrary.org/obo/vfbext/releases/2023-10-26/vfbext.json" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000078", - "lbl" : "curation status specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "curation status specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bill Bug" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000266" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000001", - "lbl" : "entity", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "entity" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "Entity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Julius Caesar" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Verdi’s Requiem" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the Second World War" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "your body mass index" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } - }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "Continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "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" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", @@ -192,62 +49,7 @@ "definition" : { "val" : "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])" }, - "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "ic" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "IndependentContinuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a chair" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a heart" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a leg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a molecule" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a spatial region" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an atom" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an orchestra." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an organism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the bottom right portion of a human torso" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the interior of your mouth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "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])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(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] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", @@ -320,18 +122,13 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a part and its whole" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - }, { - "val" : "OBO_REL:part_of" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is part of" @@ -380,15 +177,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "relationship" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" @@ -405,18 +193,13 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a whole and its part" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - }, { - "val" : "OBO_REL:has_part" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has part" @@ -444,15 +227,64 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "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" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realized in" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease is realized in this disease course" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "relationship" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is realized in this shattering" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is realized in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is realized by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "realized_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "[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])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "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" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realizes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease course realizes this disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation realizes this investigator role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this shattering realizes this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "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])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { @@ -477,7 +309,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } @@ -515,1383 +347,727 @@ "comments" : [ "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure." ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000006", - "lbl" : "material anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000003", + "lbl" : "connected anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical entity that has mass." + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." }, + "comments" : [ "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development." ], "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000007", - "lbl" : "immaterial anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000004", + "lbl" : "organism substance", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that has no mass." + "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." }, - "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] + "comments" : [ "Note - CARO explicitly declares organisms substances to be part of (some) organism." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "portion of organism substance" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle." + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0020003", - "lbl" : "cellular anatomical structure", + "id" : "http://purl.obolibrary.org/obo/CARO_0000006", + "lbl" : "material anatomical entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure consisting of one or more cells." + "val" : "An anatomical entity that has mass." }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-09-28T14:20:19Z" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0030000", - "lbl" : "biological entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000007", + "lbl" : "immaterial anatomical entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." + "val" : "Anatomical entity that has no mass." }, - "comments" : [ "Important for alignment with Darwin Core class \"Organism\"." ] + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0030002", - "lbl" : "expression pattern", + "id" : "http://purl.obolibrary.org/obo/CARO_0000012", + "lbl" : "multicellular organism", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." - } + "val" : "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." + }, + "comments" : [ "MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. \n\nMH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities." ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_00007001", - "lbl" : "anatomical structure", + "id" : "http://purl.obolibrary.org/obo/CARO_0000013", + "lbl" : "cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.", - "xrefs" : [ "CARO:MAH", "FBC:DOS" ] + "val" : "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." }, - "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], + "comments" : [ "deprecate and replace with CL or GO term?" ], "xrefs" : [ { - "val" : "CARO:0000003" + "val" : "CL:0000000" }, { - "val" : "UBERON:0000061" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "val" : "GO:0005623" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_00007016", - "lbl" : "material anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000014", + "lbl" : "cell part", "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], - "xrefs" : [ { - "val" : "CARO:0000006" - }, { - "val" : "UBERON:0000465" - } ], + "definition" : { + "val" : "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." + }, + "comments" : [ "This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "cell component" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_00100313", - "lbl" : "multicellular structure", + "id" : "http://purl.obolibrary.org/obo/CARO_0000032", + "lbl" : "organism subdivision", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that has multiple cells as parts.", - "xrefs" : [ "FBC:DOS" ] + "val" : "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." }, - "xrefs" : [ { - "val" : "UBERON:0010000" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2010-11-02T02:25:04Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/FBbt_10000000", - "lbl" : "anatomical entity", + "id" : "http://purl.obolibrary.org/obo/CARO_0000040", + "lbl" : "acellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity which is part_of Drosophila melanogaster.", - "xrefs" : [ "CARO:MAH" ] + "val" : "An anatomical structure that has no cells or cell parts as a part." }, - "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#EmbDevSlim", "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Drosophila" - } ], - "xrefs" : [ { - "val" : "UBERON:0001062" - } ], + "comments" : [ "Example. Insect cuticle, eggshell, hair." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000042", + "lbl" : "extraembryonic structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." + }, + "comments" : [ "MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: \"Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.\". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?\n" ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#plus" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001000", + "lbl" : "multi-cell-part structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." + }, + "comments" : [ "Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain." ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "FBbt_root:00000000" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "multi-cell-component structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003674", - "lbl" : "molecular_function", + "id" : "http://purl.obolibrary.org/obo/CARO_0001008", + "lbl" : "gross anatomical part", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", - "xrefs" : [ "GOC:pdt" ] + "val" : "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " }, - "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecular function" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/caro#plus" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0005554" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "10.7.2011" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003824", - "lbl" : "catalytic activity", + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "lbl" : "organism", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.", - "xrefs" : [ "GOC:vw", "ISBN:0198506732" ] + "val" : "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "enzyme activity", - "xrefs" : [ "GOC:dph", "GOC:tb" ] - } ], - "xrefs" : [ { - "val" : "Wikipedia:Enzyme" + "val" : "organism or virus or viroid" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Melissa Haendel" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "9/18/11" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0008150", - "lbl" : "biological_process", + "id" : "http://purl.obolibrary.org/obo/CARO_0010000", + "lbl" : "multicellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.", - "xrefs" : [ "GOC:pdt" ] + "val" : "An anatomical structure that has more than one cell as a part." }, - "comments" : [ "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." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "biological process" - }, { - "pred" : "hasExactSynonym", - "val" : "physiological process" - }, { - "pred" : "hasRelatedSynonym", - "val" : "single organism process" + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "djs93" }, { - "pred" : "hasRelatedSynonym", - "val" : "single-organism process" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Biological_process" - } ], + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "Sun Feb 27 10:53:00 GMT 2011" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0010004", + "lbl" : "cellular organism", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An individual member of a clade of cellular organisms." + }, + "comments" : [ "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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. " ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/24968" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_creation_date", + "val" : "7.16.2011" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0020000", + "lbl" : "disconnected anatomical group", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/caro#core" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0020003", + "lbl" : "cellular anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure consisting of one or more cells." + }, + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "jl" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-09-19T15:05:24Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0000004" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0007582" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0044699" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" + "val" : "2018-09-28T14:20:19Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016301", - "lbl" : "kinase activity", + "id" : "http://purl.obolibrary.org/obo/CARO_0030000", + "lbl" : "biological entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", - "xrefs" : [ "ISBN:0198506732" ] + "val" : "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." }, - "comments" : [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "phosphokinase activity" - } ], + "comments" : [ "Important for alignment with Darwin Core class \"Organism\"." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0030002", + "lbl" : "expression pattern", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/FBbt_00007001", + "lbl" : "anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome.", + "xrefs" : [ "https://orcid.org/0000-0001-9114-8737", "https://orcid.org/0000-0002-7073-9172" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], "xrefs" : [ { - "val" : "Reactome:R-HSA-6788855" + "val" : "CARO:0000003" }, { - "val" : "Reactome:R-HSA-6788867" + "val" : "UBERON:0000061" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "val" : "fly_anatomy.ontology" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016740", - "lbl" : "transferase activity", + "id" : "http://purl.obolibrary.org/obo/FBbt_00007016", + "lbl" : "material anatomical entity", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_yeast", "http://purl.obolibrary.org/obo/go#prokaryote_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], "xrefs" : [ { - "val" : "EC:2.-.-.-" - }, { - "val" : "Reactome:R-HSA-1483089" - }, { - "val" : "Reactome:R-HSA-1483186" - }, { - "val" : "Reactome:R-HSA-5668414" + "val" : "CARO:0000006" }, { - "val" : "Reactome:R-HSA-8868783" + "val" : "UBERON:0000465" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" + "val" : "fly_anatomy.ontology" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016772", - "lbl" : "transferase activity, transferring phosphorus-containing groups", + "id" : "http://purl.obolibrary.org/obo/FBbt_00100313", + "lbl" : "multicellular structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).", - "xrefs" : [ "GOC:jl", "ISBN:0198506732" ] + "val" : "Anatomical structure that has multiple cells as parts.", + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, - "comments" : [ "Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "xrefs" : [ { - "val" : "EC:2.7.-.-" + "val" : "UBERON:0010000" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2010-11-02T02:25:04Z" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "molecular_function" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" + "val" : "fly_anatomy.ontology" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000112", - "lbl" : "example of usage", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/FBbt_10000000", + "lbl" : "anatomical entity", + "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Anatomical entity which is part_of Drosophila melanogaster.", + "xrefs" : [ "https://orcid.org/0000-0001-9114-8737" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/fbbt#EmbDevSlim", "http://purl.obolibrary.org/obo/fbbt#cur", "http://purl.obolibrary.org/obo/fbbt#larval_OF" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "Drosophila" + } ], "xrefs" : [ { - "val" : "IAO:0000112" + "val" : "UBERON:0001062" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "FBbt_root:00000000" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "example_of_usage" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "fly_anatomy.ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "lbl" : "definition", - "type" : "PROPERTY", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0000011", + "lbl" : "planned process", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." + "val" : "A process that realizes a plan which is the concretization of a plan specification." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Injecting mice with a vaccine in order to test its efficacy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " + "val" : "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" + "val" : "Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "branch derived" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "6/11/9: Edited at workshop. Used to include: is initiated by an agent" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000112", + "lbl" : "specimen role", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "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." + "val" : "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" + "val" : "specimen role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "blood taken from animal: animal continues in study, whereas blood has role specimen.\nsomething taken from study subject, leaves the study and becomes the specimen." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "parasite example\n- when parasite in people we study people, people are subjects and parasites are specimen\n- when parasite extracted, they become subject in the following study\nspecimen can later be subject." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "GROUP: Role Branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obi-ontology/obi/issues/1013" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000293", + "lbl" : "has_specified_input", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + "val" : "The inverse property of is_specified_input_of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "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.\"" - }, - "basicPropertyValues" : [ { + "val" : "has_specified_input" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" + "val" : "has_specified_input" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "see is_input_of example_of_usage" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Larry Hunter" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Coutot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000295", + "lbl" : "is_specified_input_of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata incomplete" + "val" : "is_specified_input_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", + "id" : "http://purl.obolibrary.org/obo/OBI_0000299", + "lbl" : "has_specified_output", + "type" : "PROPERTY", "meta" : { "definition" : { - 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"pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:7326" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Melanie Courtot" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "ncbi_taxonomy" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7227", - "lbl" : "Drosophila melanogaster", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OBI_0000312", + "lbl" : "is_specified_output_of", + "type" : "PROPERTY", "meta" : { - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", - "pred" : "hasExactSynonym", - "val" : "fruit fly" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#synonym", - "pred" : "hasRelatedSynonym", - "val" : "Sophophora melanogaster" - } ], - "xrefs" : [ { - "val" : "GC_ID:1" - } ], + "definition" : { + "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "NCBITaxon:2267365" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is_specified_output_of" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "ncbi_taxonomy" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_7496", - "lbl" : "Pterygota ", - "type" : "CLASS", - "meta" : { - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#scientific_name", - "pred" : "hasExactSynonym", - "val" : "Pterygota" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is_specified_output_of" }, { - "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", - "pred" : "hasExactSynonym", - "val" : "winged insects" - } ], - "xrefs" : [ { - "val" : "GC_ID:1" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subclass" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "ncbi_taxonomy" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_85512", - "lbl" : "Dicondylia", - "type" : "CLASS", - "meta" : { - "xrefs" : [ { - "val" : "GC_ID:1" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alan Ruttenberg" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "ncbi_taxonomy" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/NCBITaxon_88770", - "lbl" : "Panarthropoda", - "type" : "CLASS", - "meta" : { - "xrefs" : [ { - "val" : "GC_ID:1" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON:Bjoern Peters" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "ncbi_taxonomy" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000293", - "lbl" : "has_specified_input", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The inverse property of is_specified_input_of" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000295", - "lbl" : "is_specified_input_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000299", - "lbl" : "has_specified_output", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The inverse property of is_specified_output_of" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000312", - "lbl" : "is_specified_output_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." - } - } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000417", - "lbl" : "achieves_planned_objective", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0000833", - "lbl" : "objective_achieved_by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000001", - "lbl" : "quality", - "type" : "CLASS", + "lbl" : "achieves_planned_objective", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.", - "xrefs" : [ "PATOC:GVG" ] + "val" : "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trait" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0000072" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "achieves_planned_objective" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A cell sorting process achieves the objective specification 'material separation objective'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000120" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "BP, AR, PPPB branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "PPPB branch derived" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000125", - "lbl" : "mass", + "id" : "http://purl.obolibrary.org/obo/OBI_0000659", + "lbl" : "specimen collection process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.", - "xrefs" : [ "PATOC:GVG" ] + "val" : "A planned process with the objective of collecting a specimen." }, - "comments" : [ "For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism." ], - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim", "http://purl.obolibrary.org/obo/pato#relational_slim", "http://purl.obolibrary.org/obo/pato#scalar_slim" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "specimen collection process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Philly2013: The specimen_role for the specimen is created during the specimen collection process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "label changed to 'specimen collection process' on 10/27/2014, details see tracker:\nhttp://sourceforge.net/p/obi/obi-terms/716/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "specimen collection" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "6/9/09: used at workshop" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001018", - "lbl" : "physical quality", + "id" : "http://purl.obolibrary.org/obo/OBI_0000684", + "lbl" : "specimen collection objective", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.", - "xrefs" : [ "PATOC:GVG" ] + "val" : "A objective specification to obtain a material entity for potential use as an input during an investigation." }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "relational physical quality" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Physical_property" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0002079" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "specimen collection objective" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Bjoern Peters" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Bjoern Peters" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001241", - "lbl" : "physical object quality", + "id" : "http://purl.obolibrary.org/obo/OBI_0002076", + "lbl" : "collection of specimens", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A quality which inheres in a continuant.", - "xrefs" : [ "PATOC:GVG" ] + "val" : "A material entity that has two or more specimens as its parts." }, - "comments" : [ "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." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "monadic quality of a continuant" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "collection of specimens" }, { - "pred" : "hasExactSynonym", - "val" : "multiply inhering quality of a physical entity" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Blood cells collected from multiple donors over the course of a study." }, { - "pred" : "hasExactSynonym", - "val" : "multiply inhering quality of a physical entity " + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "hasExactSynonym", - "val" : "quality of a continuant" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/" }, { - "pred" : "hasExactSynonym", - "val" : "quality of a single physical entity" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Chris Stoeckert, Jie Zheng" }, { - "pred" : "hasExactSynonym", - "val" : "quality of an object" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "OBIB, OBI" }, { - "pred" : "hasExactSynonym", - "val" : "quality of continuant" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "Biobank" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBI_0100051", + "lbl" : "specimen", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity that has the specimen role." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "specimen" }, { - "pred" : "hasNarrowSynonym", - "val" : "monadic quality of an object" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." }, { - "pred" : "hasNarrowSynonym", - "val" : "monadic quality of continuant" - } ], - "xrefs" : [ { - "val" : "snap:Quality" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001237" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "PATO:0001238" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: James Malone" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "PERSON: Philippe Rocca-Serra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GROUP: OBI Biomaterial Branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obi-ontology/obi/issues/1013" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic_of", + "lbl" : "characteristic of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." }, "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], - "xrefs" : [ { - "val" : "RO:0000052" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "inheres in" @@ -1907,25 +1083,16 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "characteristic_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has_characteristic", + "lbl" : "has characteristic", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of characteristic_of" }, - "xrefs" : [ { - "val" : "RO:0000053" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "bearer of" @@ -1947,12 +1114,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_characteristic" } ] } }, { @@ -2007,10 +1168,42 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "lbl" : "is concretized as", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "lbl" : "concretizes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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)." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000079", "lbl" : "function of", @@ -2379,9 +1572,6 @@ "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002131" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -2391,12 +1581,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "overlaps" } ] } }, { @@ -2453,9 +1637,6 @@ "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002211" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-7476-6306" @@ -2480,9 +1661,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "false" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "gene_ontology" } ] } }, { @@ -2494,9 +1672,6 @@ "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002212" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" @@ -2509,9 +1684,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "gene_ontology" } ] } }, { @@ -2523,9 +1695,6 @@ "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002213" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" @@ -2538,23 +1707,17 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "gene_ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable_of", + "lbl" : "capable of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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. " }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002215" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" @@ -2576,37 +1739,22 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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)\"." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002216", - "lbl" : "capable_of_part_of", + "lbl" : "capable of part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, - "xrefs" : [ { - "val" : "RO:0002216" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function in" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of_part_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -2705,21 +1853,12 @@ "definition" : { "val" : "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." }, - "xrefs" : [ { - "val" : "RO:0002292" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "fly_anatomy.ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "expresses" } ] } }, { @@ -3687,19 +2826,6 @@ "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002610", - "lbl" : "correlated with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "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." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Groups both positive and negative correlation" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "lbl" : "directly positively regulates", @@ -3746,6 +2872,22 @@ "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004031", "lbl" : "enables subfunction", @@ -3838,52 +2980,145 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:53:22Z" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" + "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004046", - "lbl" : "causally upstream of or within, negative effect", + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "lbl" : "generically depends on", "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "g-depends on" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Genetic information generically depend on molecules of DNA." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The novel *War and Peace* generically depends on this copy of the novel." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:55:05Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The pattern shared by chess boards generically depends on any chess board." }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", 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"http://purl.obolibrary.org/obo/OBI_0000112", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_85512" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_85512", + "sub" : "http://purl.obolibrary.org/obo/OBI_0000659", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_50557" + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { - "sub" : "http://purl.obolibrary.org/obo/NCBITaxon_88770", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_1206794" + "sub" : "http://purl.obolibrary.org/obo/OBI_0000659", + "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000001", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + "sub" : "http://purl.obolibrary.org/obo/OBI_0000659", + "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100051" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000125", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" + "sub" : "http://purl.obolibrary.org/obo/OBI_0000659", + "pred" : "http://purl.obolibrary.org/obo/OBI_0000417", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000684" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001018", + "sub" : "http://purl.obolibrary.org/obo/OBI_0000684", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" + "obj" : "http://purl.obolibrary.org/obo/IAO_0000005" }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001241", + "sub" : "http://purl.obolibrary.org/obo/OBI_0002076", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000001" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "sub" : "http://purl.obolibrary.org/obo/OBI_0100051", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000465", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001062" + "sub" : "http://purl.obolibrary.org/obo/OBI_0100051", + "pred" : "http://purl.obolibrary.org/obo/RO_0000087", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000112" }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "sub" : "http://purl.obolibrary.org/obo/SO_0000110", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_10000005", "pred" : "is_a", @@ -4564,14 +3649,6 @@ "sub" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014", "pred" : "is_a", "obj" : "http://xmlns.com/foaf/0.1/image" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000125", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000428", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000078" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "subPropertyOf", @@ -5028,6 +4105,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002630", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004028", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002410" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004031", "pred" : "subPropertyOf", @@ -5064,6 +4145,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004047", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0009501", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002410" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0011002", "pred" : "subPropertyOf", @@ -5080,10 +4165,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012012", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012011" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0017003", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002610" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0019000", "pred" : "subPropertyOf", @@ -5116,6 +4197,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000055" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000062", "pred" : "inverseOf", @@ -5128,6 +4213,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000056", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000058", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000059" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000079", "pred" : "inverseOf", @@ -5208,14 +4297,35 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002559", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002566" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0010001", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0010002" } ], "logicalDefinitionAxioms" : [ { + "definedClassId" : "http://purl.obolibrary.org/obo/CARO_0000003", + "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0002266" + }, { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0010000" + } ] + }, { "definedClassId" : "http://purl.obolibrary.org/obo/CARO_0000006", "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000125" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CARO_0010000", + "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001993" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/FBbt_10000000", "genusIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], @@ -5223,6 +4333,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0000659", + "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000417", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000684" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0100051", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000087", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000112" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004", "genusIds" : [ "http://purl.obolibrary.org/obo/FBbt_00100313" ], @@ -5262,6 +4386,14 @@ "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000055", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000062", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -5278,6 +4410,14 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000059", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ] @@ -5360,6 +4500,22 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002595", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0011002", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -5396,6 +4552,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000055", "http://purl.obolibrary.org/obo/RO_0000052" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -5405,9 +4564,18 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002584", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000054", "http://purl.obolibrary.org/obo/RO_0002404" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/RO_0000058" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -5540,6 +4708,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] } ] } ] } \ No newline at end of file diff --git a/vfbext.obo b/vfbext.obo index 606277d..46a6a76 100644 --- a/vfbext.obo +++ b/vfbext.obo @@ -1,23 +1,9 @@ format-version: 1.2 -date: 15:08:2023 10:37 -subsetdef: attribute_slim "" +date: 26:10:2023 13:58 subsetdef: clone "" -subsetdef: common_anatomy "" subsetdef: core "" subsetdef: cur "" subsetdef: EmbDevSlim "" -subsetdef: goslim_agr "" -subsetdef: goslim_candida "" -subsetdef: goslim_chembl "" -subsetdef: goslim_drosophila "" -subsetdef: goslim_flybase_ribbon "" -subsetdef: goslim_generic "" -subsetdef: goslim_metagenomics "" -subsetdef: goslim_mouse "" -subsetdef: goslim_pir "" -subsetdef: goslim_plant "" -subsetdef: goslim_pombe "" -subsetdef: goslim_yeast "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -25,96 +11,40 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: larval_OF "" subsetdef: neuron "" subsetdef: ns_part "" -subsetdef: prokaryote_subset "" -subsetdef: relational_slim "" +subsetdef: plus "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" -subsetdef: scalar_slim "" subsetdef: synaptic_neuropil "" subsetdef: tract "" -subsetdef: upper_level "" -synonymtypedef: blast_name "" -synonymtypedef: common_name "" -synonymtypedef: genbank_common_name "" -synonymtypedef: in_part "" -synonymtypedef: scientific_name "" -synonymtypedef: synonym "" remark: VFB extension ontology ontology: http://virtualflybrain.org/data/VFB/OWL/vfbext.owl property_value: http://purl.org/dc/elements/1.1/description "An ontology of miscellaneous terms for data annotation in VFB." xsd:string property_value: http://purl.org/dc/elements/1.1/title "VFB Extension Ontology" xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2023-08-15" xsd:string - -[Term] -id: BFO:0000001 -name: entity -property_value: BFO:0000179 "entity" xsd:string -property_value: BFO:0000180 "Entity" xsd:string -property_value: editor_note "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: editor_note "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: example_of_usage "Julius Caesar" xsd:string -property_value: example_of_usage "the Second World War" xsd:string -property_value: example_of_usage "Verdi’s Requiem" xsd:string -property_value: example_of_usage "your body mass index" xsd:string -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 +property_value: owl:versionInfo "2023-10-26" xsd:string [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." [] -is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: part_of BFO:0000002 {all_only="true"} ! continuant -property_value: BFO:0000179 "continuant" xsd:string -property_value: BFO:0000180 "Continuant" xsd:string -property_value: editor_note "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: editor_note "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 +relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: part_of BFO:0000003 {all_only="true"} ! occurrent +relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent [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." [] -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"} +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])" [] comment: 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 disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000004 {all_only="true"} ! independent continuant -property_value: BFO:0000179 "ic" xsd:string -property_value: BFO:0000180 "IndependentContinuant" xsd:string -property_value: example_of_usage "a chair" xsd:string -property_value: example_of_usage "a heart" xsd:string -property_value: example_of_usage "a leg" xsd:string -property_value: example_of_usage "a molecule" xsd:string -property_value: example_of_usage "a spatial region" xsd:string -property_value: example_of_usage "an atom" xsd:string -property_value: example_of_usage "an orchestra." xsd:string -property_value: example_of_usage "an organism" xsd:string -property_value: example_of_usage "the bottom right portion of a human torso" xsd:string -property_value: example_of_usage "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 +relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant [Term] id: BFO:0000015 @@ -135,13 +65,13 @@ name: realizable entity def: "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." [] is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality -relationship: part_of BFO:0000017 {all_only="true"} ! realizable entity +relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant -relationship: part_of BFO:0000019 {all_only="true"} ! quality +relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 @@ -150,7 +80,7 @@ def: "b is a specifically dependent continuant = Def. b is a continuant & there comment: 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 disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000020 {all_only="true"} ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant [Term] id: BFO:0000023 @@ -164,7 +94,7 @@ 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])" [] comment: 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. is_a: BFO:0000002 ! continuant -relationship: part_of BFO:0000031 {all_only="true"} ! generically dependent continuant +relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant [Term] id: BFO:0000034 @@ -190,6 +120,29 @@ def: "A part of a cellular organism that is either an immaterial entity or a mat comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. is_a: CARO:0030000 ! biological entity +[Term] +id: CARO:0000003 +name: connected anatomical structure +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [] +comment: Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. +subset: core +is_a: CARO:0000006 ! material anatomical entity +intersection_of: CARO:0000006 ! material anatomical entity +intersection_of: RO:0000053 PATO:0002266 ! has characteristic +intersection_of: RO:0000053 PATO:0010000 ! has characteristic +disjoint_from: CARO:0000004 ! organism substance +relationship: RO:0000053 PATO:0002266 ! has characteristic +relationship: RO:0000053 PATO:0010000 ! has characteristic + +[Term] +id: CARO:0000004 +name: organism substance +def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome." [] +comment: Note - CARO explicitly declares organisms substances to be part of (some) organism. +synonym: "portion of organism substance" EXACT [] +is_a: CARO:0001008 ! gross anatomical part +property_value: IAO:0000112 "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle." xsd:string + [Term] id: CARO:0000006 name: material anatomical entity @@ -197,9 +150,9 @@ def: "An anatomical entity that has mass." [] subset: core is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity -intersection_of: has_characteristic PATO:0000125 ! mass +intersection_of: RO:0000053 PATO:0000125 ! has characteristic disjoint_from: CARO:0000007 ! immaterial anatomical entity -relationship: has_characteristic PATO:0000125 ! mass +relationship: RO:0000053 PATO:0000125 ! has characteristic [Term] id: CARO:0000007 @@ -209,6 +162,144 @@ subset: core is_a: BFO:0000141 ! immaterial entity is_a: CARO:0000000 ! anatomical entity +[Term] +id: CARO:0000012 +name: multicellular organism +def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] +comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. \n\nMH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. +is_a: CARO:0010004 ! cellular organism + +[Term] +id: CARO:0000013 +name: cell +def: "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [] +comment: deprecate and replace with CL or GO term? +xref: CL:0000000 +xref: GO:0005623 +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0020003 ! cellular anatomical structure +disjoint_from: CARO:0000014 ! cell part +disjoint_from: CARO:0000040 ! acellular anatomical structure +disjoint_from: CARO:0000042 ! extraembryonic structure +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure + +[Term] +id: CARO:0000014 +name: cell part +def: "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher." [] +comment: This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class. +is_a: CARO:0000003 ! connected anatomical structure +disjoint_from: CARO:0000040 ! acellular anatomical structure +disjoint_from: CARO:0000042 ! extraembryonic structure +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 CARO:0000013 ! part of cell +property_value: IAO:0000118 "cell component" xsd:string + +[Term] +id: CARO:0000032 +name: organism subdivision +def: "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [] +subset: core +is_a: CARO:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism." xsd:string + +[Term] +id: CARO:0000040 +name: acellular anatomical structure +def: "An anatomical structure that has no cells or cell parts as a part." [] +comment: Example. Insect cuticle, eggshell, hair. +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001008 ! gross anatomical part +intersection_of: CARO:0000003 ! connected anatomical structure +intersection_of: RO:0002180 CARO:0000013 {cardinality="0"} ! has component cell +intersection_of: RO:0002180 CARO:0000014 {cardinality="0"} ! has component cell part +disjoint_from: CARO:0000042 ! extraembryonic structure +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure + +[Term] +id: CARO:0000042 +name: extraembryonic structure +def: "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." [] +comment: MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids?\n +subset: plus +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001008 ! gross anatomical part +disjoint_from: CARO:0001000 ! multi-cell-part structure +disjoint_from: CARO:0010000 ! multicellular anatomical structure + +[Term] +id: CARO:0001000 +name: multi-cell-part structure +def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [] +comment: Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain. +subset: core +is_a: CARO:0001008 ! gross anatomical part +disjoint_from: CARO:0010000 ! multicellular anatomical structure +property_value: IAO:0000118 "multi-cell-component structure" xsd:string + +[Term] +id: CARO:0001008 +name: gross anatomical part +def: "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. " [] +subset: plus +is_a: CARO:0000006 ! material anatomical entity +union_of: CARO:0000004 ! organism substance +union_of: CARO:0000032 ! organism subdivision +union_of: CARO:0000040 ! acellular anatomical structure +union_of: CARO:0000042 ! extraembryonic structure +union_of: CARO:0001000 ! multi-cell-part structure +union_of: CARO:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 CARO:0000012 ! part of multicellular organism +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.7.2011" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 + +[Term] +id: CARO:0001010 +name: organism +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +synonym: "organism or virus or viroid" EXACT [] +is_a: BFO:0000040 ! material entity +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000117 "Melissa Haendel" xsd:string + +[Term] +id: CARO:0010000 +name: multicellular anatomical structure +def: "An anatomical structure that has more than one cell as a part." [] +subset: core +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001008 ! gross anatomical part +intersection_of: CARO:0000003 {comment="There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS"} ! connected anatomical structure +intersection_of: RO:0000053 PATO:0001993 {comment="There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS"} ! has characteristic +relationship: RO:0000053 PATO:0001993 ! has characteristic +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "Sun Feb 27 10:53:00 GMT 2011" xsd:string +property_value: IAO:0000117 "djs93" xsd:string + +[Term] +id: CARO:0010004 +name: cellular organism +def: "An individual member of a clade of cellular organisms." [] +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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +is_a: CARO:0000003 ! connected anatomical structure +is_a: CARO:0001010 ! organism +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 + +[Term] +id: CARO:0020000 +name: disconnected anatomical group +def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [] +subset: core +is_a: CARO:0000006 ! material anatomical entity +intersection_of: CARO:0000006 ! material anatomical entity +intersection_of: RO:0000053 PATO:0010001 ! has characteristic +intersection_of: RO:0002180 CARO:0000003 {minCardinality="2"} ! has component connected anatomical structure +relationship: RO:0000053 PATO:0010001 ! has characteristic +relationship: RO:0002180 CARO:0000003 ! has component connected anatomical structure + [Term] id: CARO:0020003 name: cellular anatomical structure @@ -229,12 +320,13 @@ id: CARO:0030002 name: expression pattern def: "The mereological sum of all cells in a single organism in which expression of some specified gene occurs." [] is_a: CARO:0020003 ! cellular anatomical structure +relationship: BFO:0000051 CARO:0000013 ! has part cell [Term] id: FBbt:00007001 name: anatomical structure namespace: fly_anatomy.ontology -def: "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome." [CARO:MAH, FBC:DOS] +def: "Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome." [https://orcid.org/0000-0001-9114-8737, https://orcid.org/0000-0002-7073-9172] subset: cur subset: larval_OF xref: CARO:0000003 @@ -255,10 +347,10 @@ is_a: FBbt:10000000 ! anatomical entity id: FBbt:00100313 name: multicellular structure namespace: fly_anatomy.ontology -def: "Anatomical structure that has multiple cells as parts." [FBC:DOS] +def: "Anatomical structure that has multiple cells as parts." [https://orcid.org/0000-0002-7073-9172] xref: UBERON:0010000 is_a: FBbt:00007001 ! anatomical structure -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 property_value: http://purl.org/dc/terms/date "2010-11-02T02:25:04Z" xsd:dateTime [Term] @@ -266,7 +358,7 @@ id: FBbt:10000000 name: anatomical entity namespace: fly_anatomy.ontology alt_id: FBbt_root:00000000 -def: "Anatomical entity which is part_of Drosophila melanogaster." [CARO:MAH] +def: "Anatomical entity which is part_of Drosophila melanogaster." [https://orcid.org/0000-0001-9114-8737] subset: cur subset: EmbDevSlim subset: larval_OF @@ -274,546 +366,118 @@ synonym: "Drosophila" RELATED [] xref: UBERON:0001062 is_a: CARO:0000000 ! anatomical entity intersection_of: CARO:0000000 ! anatomical entity -intersection_of: part_of NCBITaxon:7227 ! Drosophila melanogaster -disjoint_from: PATO:0000001 ! quality -relationship: part_of NCBITaxon:7227 ! Drosophila melanogaster - -[Term] -id: GO:0003674 -name: molecular_function -namespace: molecular_function -alt_id: GO:0005554 -def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." [GOC:pdt] -comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. -subset: goslim_candida -subset: goslim_chembl -subset: goslim_metagenomics -subset: goslim_pir -subset: goslim_plant -subset: goslim_yeast -synonym: "molecular function" EXACT [] - -[Term] -id: GO:0003824 -name: catalytic activity -namespace: molecular_function -def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [GOC:vw, ISBN:0198506732] -subset: goslim_agr -subset: goslim_chembl -subset: goslim_flybase_ribbon -subset: goslim_generic -subset: goslim_metagenomics -subset: goslim_pir -subset: goslim_plant -synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] -xref: Wikipedia:Enzyme -is_a: GO:0003674 ! molecular_function +intersection_of: BFO:0000050 NCBITaxon:7227 ! part of +disjoint_from: PATO:0000001 +relationship: BFO:0000050 NCBITaxon:7227 ! part of [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 is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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_candida -subset: goslim_chembl -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: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI -created_by: jl -creation_date: 2012-09-19T15:05:24Z +disjoint_from: OBI:0000011 ! planned process [Term] id: GO:0016301 -name: kinase activity -namespace: molecular_function -def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] -comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_metagenomics -subset: goslim_plant -subset: goslim_yeast -synonym: "phosphokinase activity" EXACT [] -xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm" -xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines" -is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups - -[Term] -id: GO:0016740 -name: transferase activity -namespace: molecular_function -def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732] -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_generic -subset: goslim_metagenomics -subset: goslim_mouse -subset: goslim_pir -subset: goslim_plant -subset: goslim_yeast -subset: prokaryote_subset -xref: EC:2.-.-.- -xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2" -xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1" -xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK" -xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248" -is_a: GO:0003824 ! catalytic activity [Term] -id: GO:0016772 -name: transferase activity, transferring phosphorus-containing groups -namespace: molecular_function -def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732] -comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. -subset: goslim_chembl -xref: EC:2.7.-.- -is_a: GO:0016740 ! transferase activity - -[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." [] -property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string -property_value: IAO:0000111 "curation status specification" xsd:string +id: OBI:0000011 +name: planned process +def: "A process that realizes a plan which is the concretization of a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string +property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000119 "branch derived" xsd:string +property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string +property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + +[Term] +id: OBI:0000112 +name: specimen role +def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] +is_a: BFO:0000023 ! role +property_value: IAO:0000111 "specimen role" xsd:string +property_value: IAO:0000112 "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role." xsd:string +property_value: IAO:0000116 "blood taken from animal: animal continues in study, whereas blood has role specimen.\nsomething taken from study subject, leaves the study and becomes the specimen." xsd:string +property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string +property_value: IAO:0000116 "parasite example\n- when parasite in people we study people, people are subjects and parasites are specimen\n- when parasite extracted, they become subject in the following study\nspecimen can later be subject." xsd:string +property_value: IAO:0000117 "GROUP: Role Branch" xsd:string +property_value: IAO:0000119 "OBI" xsd:string +property_value: IAO:0000233 https://github.com/obi-ontology/obi/issues/1013 + +[Term] +id: OBI:0000659 +name: specimen collection process +def: "A planned process with the objective of collecting a specimen." [] +is_a: OBI:0000011 ! planned process +intersection_of: OBI:0000011 ! planned process +intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective +relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity +relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen +relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective +property_value: IAO:0000111 "specimen collection process" xsd:string +property_value: IAO:0000112 "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "label changed to 'specimen collection process' on 10/27/2014, details see tracker:\nhttp://sourceforge.net/p/obi/obi-terms/716/" xsd:string +property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string +property_value: IAO:0000116 "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role." xsd:string +property_value: IAO:0000116 "Philly2013: The specimen_role for the specimen is created during the specimen collection process." xsd:string +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000118 "specimen collection" xsd:string +property_value: IAO:0000232 "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession" xsd:string +property_value: IAO:0000232 "6/9/09: used at workshop" xsd:string + +[Term] +id: OBI:0000684 +name: specimen collection objective +def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] +is_a: IAO:0000005 +property_value: IAO:0000111 "specimen collection objective" xsd:string +property_value: IAO:0000112 "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Bjoern Peters" xsd:string +property_value: IAO:0000119 "Bjoern Peters" xsd:string + +[Term] +id: OBI:0002076 +name: collection of specimens +def: "A material entity that has two or more specimens as its parts." [] +is_a: BFO:0000040 ! material entity +intersection_of: BFO:0000040 ! material entity +intersection_of: RO:0002351 OBI:0100051 {all_only="true"} ! has member specimen +property_value: http://purl.org/dc/elements/1.1/source "Biobank" xsd:string +property_value: IAO:0000111 "collection of specimens" xsd:string +property_value: IAO:0000112 "Blood cells collected from multiple donors over the course of a study." xsd:string property_value: IAO:0000114 IAO:0000125 -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: NCBITaxon:1 -name: root -namespace: ncbi_taxonomy -synonym: "all" RELATED synonym [] -xref: GC_ID:1 - -[Term] -id: NCBITaxon:1206794 -name: Ecdysozoa -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33317 ! Protostomia -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:131567 -name: cellular organisms -namespace: ncbi_taxonomy -synonym: "biota" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:1 ! root - -[Term] -id: NCBITaxon:197562 -name: Pancrustacea -namespace: ncbi_taxonomy -xref: GC_ID:1 -xref: PMID:10874751 -xref: PMID:11557979 -is_a: NCBITaxon:197563 ! Mandibulata -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:197563 -name: Mandibulata -namespace: ncbi_taxonomy -synonym: "mandibulates" EXACT common_name [] -xref: GC_ID:1 -xref: PMID:11557979 -xref: PMID:9727836 -is_a: NCBITaxon:6656 ! Arthropoda -property_value: has_rank NCBITaxon:clade - -[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 -xref: PMID:30257078 -is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom - -[Term] -id: NCBITaxon:32341 -name: Sophophora -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7215 ! Drosophila -property_value: has_rank NCBITaxon:subgenus - -[Term] -id: NCBITaxon:32346 -name: melanogaster group -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:32341 ! Sophophora -property_value: has_rank NCBITaxon:species_group - -[Term] -id: NCBITaxon:32351 -name: melanogaster subgroup -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:32346 ! melanogaster group -property_value: has_rank NCBITaxon:species_subgroup - -[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: has_rank NCBITaxon:clade - -[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 - -[Term] -id: NCBITaxon:33213 -name: Bilateria -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:33317 -name: Protostomia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:33340 -name: Neoptera -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7496 ! Pterygota -property_value: has_rank NCBITaxon:infraclass - -[Term] -id: NCBITaxon:33392 -name: Endopterygota -namespace: ncbi_taxonomy -synonym: "Holometabola" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:33340 ! Neoptera -property_value: has_rank NCBITaxon:cohort - -[Term] -id: NCBITaxon:43733 -name: Muscomorpha -namespace: ncbi_taxonomy -alt_id: NCBITaxon:43732 -synonym: "Asilomorpha" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:7203 ! Brachycera -property_value: has_rank NCBITaxon:infraorder - -[Term] -id: NCBITaxon:43738 -name: Schizophora -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:480117 ! Cyclorrhapha - -[Term] -id: NCBITaxon:43741 -name: Acalyptratae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43738 ! Schizophora - -[Term] -id: NCBITaxon:43746 -name: Ephydroidea -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43741 ! Acalyptratae -property_value: has_rank NCBITaxon:superfamily - -[Term] -id: NCBITaxon:43845 -name: Drosophilinae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7214 ! Drosophilidae -property_value: has_rank NCBITaxon:subfamily - -[Term] -id: NCBITaxon:46877 -name: Drosophilini -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43845 ! Drosophilinae -property_value: has_rank NCBITaxon:tribe - -[Term] -id: NCBITaxon:480117 -name: Cyclorrhapha -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:480118 ! Eremoneura -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:480118 -name: Eremoneura -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:43733 ! Muscomorpha -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:50557 -name: Insecta -namespace: ncbi_taxonomy -synonym: "insects" RELATED blast_name [] -synonym: "true insects" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:6960 ! Hexapoda -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:6072 -name: Eumetazoa -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade +property_value: IAO:0000116 "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/" xsd:string +property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string +property_value: IAO:0000119 "OBIB, OBI" xsd:string [Term] -id: NCBITaxon:6656 -name: Arthropoda -namespace: ncbi_taxonomy -synonym: "arthropods" EXACT genbank_common_name [] -synonym: "arthropods" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:88770 ! Panarthropoda -property_value: has_rank NCBITaxon:phylum - -[Term] -id: NCBITaxon:6960 -name: Hexapoda -namespace: ncbi_taxonomy -synonym: "Atelocerata" RELATED in_part [] -synonym: "hexapods" RELATED blast_name [] -synonym: "insects" EXACT genbank_common_name [] -synonym: "Tracheata" RELATED in_part [] -synonym: "Uniramia" RELATED in_part [] -xref: GC_ID:1 -is_a: NCBITaxon:197562 ! Pancrustacea -property_value: has_rank NCBITaxon:subphylum - -[Term] -id: NCBITaxon:7147 -name: Diptera -namespace: ncbi_taxonomy -synonym: "flies" EXACT genbank_common_name [] -synonym: "flies" RELATED blast_name [] -xref: GC_ID:1 -is_a: NCBITaxon:33392 ! Endopterygota -property_value: has_rank NCBITaxon:order - -[Term] -id: NCBITaxon:7203 -name: Brachycera -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7147 ! Diptera -property_value: has_rank NCBITaxon:suborder - -[Term] -id: NCBITaxon:7214 -name: Drosophilidae -namespace: ncbi_taxonomy -synonym: "pomace flies" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:43746 ! Ephydroidea -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:7215 -name: Drosophila -namespace: ncbi_taxonomy -alt_id: NCBITaxon:7326 -synonym: "Drosophila" EXACT scientific_name [] -synonym: "fruit flies" EXACT genbank_common_name [] -synonym: "fruit fly" EXACT common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:46877 ! Drosophilini -property_value: has_rank NCBITaxon:genus - -[Term] -id: NCBITaxon:7227 -name: Drosophila melanogaster -namespace: ncbi_taxonomy -alt_id: NCBITaxon:2267365 -synonym: "fruit fly" EXACT genbank_common_name [] -synonym: "Sophophora melanogaster" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:32351 ! melanogaster subgroup -property_value: has_rank NCBITaxon:species - -[Term] -id: NCBITaxon:7496 -name: Pterygota -namespace: ncbi_taxonomy -synonym: "Pterygota" EXACT scientific_name [] -synonym: "winged insects" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:85512 ! Dicondylia -property_value: has_rank NCBITaxon:subclass - -[Term] -id: NCBITaxon:85512 -name: Dicondylia -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:50557 ! Insecta -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:88770 -name: Panarthropoda -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1206794 ! Ecdysozoa -property_value: has_rank NCBITaxon:clade - -[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] -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 [] -is_a: BFO:0000020 ! specifically dependent continuant - -[Term] -id: PATO:0000125 -name: mass -namespace: quality -def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [PATOC:GVG] -comment: For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. -subset: attribute_slim -subset: relational_slim -subset: scalar_slim -is_a: PATO:0001018 ! physical quality - -[Term] -id: PATO:0001018 -name: physical quality -namespace: quality -alt_id: PATO:0002079 -def: "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] -subset: attribute_slim -synonym: "relational physical quality" EXACT [] -xref: Wikipedia:Physical_property -is_a: PATO:0001241 ! physical object quality - -[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: "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 - -[Term] -id: UBERON:0000465 -name: material anatomical entity -def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] -subset: common_anatomy -subset: upper_level -xref: AAO:0010264 -xref: AEO:0000006 -xref: BILA:0000006 -xref: CARO:0000006 -xref: EHDAA2:0003006 -xref: FBbt:00007016 -xref: FMA:67165 -xref: HAO:0000006 -xref: TAO:0001836 -xref: TGMA:0001826 -xref: VHOG:0001721 +id: OBI:0100051 +name: specimen +def: "A material entity that has the specimen role." [] +is_a: BFO:0000040 ! material entity +intersection_of: BFO:0000040 ! material entity +intersection_of: RO:0000087 OBI:0000112 ! has role specimen role +relationship: RO:0000087 OBI:0000112 ! has role specimen role +property_value: IAO:0000111 "specimen" xsd:string +property_value: IAO:0000112 "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string +property_value: IAO:0000117 "PERSON: James Malone" xsd:string +property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string +property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string +property_value: IAO:0000233 https://github.com/obi-ontology/obi/issues/1013 + +[Term] +id: SO:0000110 is_a: BFO:0000040 ! material entity -is_a: UBERON:0001062 ! anatomical entity -property_value: RO:0002175 NCBITaxon:33090 -property_value: RO:0002175 NCBITaxon:4751 - -[Term] -id: UBERON:0001062 -name: anatomical entity -def: "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." [FMA:62955, http://orcid.org/0000-0001-9114-8737] -subset: common_anatomy -subset: upper_level -xref: AAO:0010841 -xref: AEO:0000000 -xref: BILA:0000000 -xref: BIRNLEX:6 -xref: CARO:0000000 -xref: EHDAA2:0002229 -xref: FBbt:10000000 -xref: FMA:62955 -xref: HAO:0000000 -xref: MA:0000001 -xref: NCIT:C12219 -xref: TAO:0100000 -xref: TGMA:0001822 -xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} -xref: WBbt:0000100 -xref: XAO:0000000 -xref: ZFA:0100000 -is_a: BFO:0000004 ! independent continuant -property_value: RO:0002175 NCBITaxon:33090 -property_value: RO:0002175 NCBITaxon:4751 [Term] id: VFB:10000005 @@ -826,8 +490,8 @@ name: expression pattern fragment comment: A multicellular structure that is part of an expression pattern. is_a: FBbt:00100313 ! multicellular structure intersection_of: FBbt:00100313 ! multicellular structure -intersection_of: part_of CARO:0030002 ! expression pattern -relationship: part_of CARO:0030002 ! expression pattern +intersection_of: BFO:0000050 CARO:0030002 ! part of expression pattern +relationship: BFO:0000050 CARO:0030002 ! part of expression pattern created_by: dos creation_date: 2018-03-04T10:55:59Z @@ -856,19 +520,99 @@ id: VFBext:0000014 name: channel is_a: http://xmlns.com/foaf/0.1/image +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: 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 +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI +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" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" 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: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: BFO:0000054 +name: realized in +comment: 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 +property_value: IAO:0000111 "realized in" xsd:string +property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string +property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string +property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string +property_value: IAO:0000118 "is realized by" xsd:string +property_value: IAO:0000118 "realized_in" xsd:string +property_value: IAO:0000600 "[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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +inverse_of: BFO:0000055 ! realizes + +[Typedef] +id: BFO:0000055 +name: realizes +comment: 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 +property_value: IAO:0000111 "realizes" xsd:string +property_value: IAO:0000112 "this disease course realizes this disease" xsd:string +property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string +property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string +property_value: IAO:0000600 "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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +domain: BFO:0000015 ! process +range: BFO:0000017 ! realizable entity + [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: editor_note "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: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/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 domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000062 +holds_over_chain: BFO:0000050 BFO:0000062 is_transitive: true is_a: RO:0002086 ! ends after inverse_of: BFO:0000063 ! precedes @@ -881,7 +625,7 @@ subset: ro-eco property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000063 +holds_over_chain: BFO:0000050 BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to @@ -889,44 +633,102 @@ is_a: RO:0002222 ! temporally related to id: OBI:0000293 name: has_specified_input def: "The inverse property of is_specified_input_of" [] +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000111 "has_specified_input" xsd:string +property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl is_a: RO:0000057 ! has participant [Typedef] id: OBI:0000295 name: is_specified_input_of def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "is_specified_input_of" xsd:string +property_value: IAO:0000112 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000111 "has_specified_output" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string +property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl is_a: RO:0000057 ! has participant [Typedef] id: OBI:0000312 name: is_specified_output_of def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000111 "is_specified_output_of" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] +property_value: IAO:0000111 "achieves_planned_objective" xsd:string +property_value: IAO:0000112 "A cell sorting process achieves the objective specification 'material separation objective'" xsd:string +property_value: IAO:0000114 IAO:0000120 +property_value: IAO:0000117 "BP, AR, PPPB branch" xsd:string +property_value: IAO:0000119 "PPPB branch derived" xsd:string +property_value: IAO:0000232 "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" xsd:string [Typedef] -id: OBI:0000833 -name: objective_achieved_by -def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] +id: RO:0000052 +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: RO:0002314 ! characteristic of part of +inverse_of: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000053 +name: has characteristic +def: "Inverse of characteristic_of" [] +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: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant +is_inverse_functional: true [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: example_of_usage "this blood clot participates in this blood coagulation" xsd:string -property_value: example_of_usage "this input material (or this output material) participates in this process" xsd:string -property_value: example_of_usage "this investigator participates in this investigation" xsd:string 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 domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent @@ -936,28 +738,47 @@ inverse_of: RO:0000057 ! has participant 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: editor_note "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: example_of_usage "this blood coagulation has participant this blood clot" xsd:string -property_value: example_of_usage "this investigation has participant this investigator" xsd:string -property_value: example_of_usage "this process has participant this input material (or this output material)" xsd:string -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/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 domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant -holds_over_chain: has_part RO:0000057 +holds_over_chain: BFO:0000051 RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant [Typedef] id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function [Typedef] @@ -965,11 +786,11 @@ 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" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: example_of_usage "this red color is a quality of this apple" xsd:string +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 -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of inverse_of: RO:0000086 ! has quality [Typedef] @@ -977,44 +798,44 @@ id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this investigator role is a role of this person" xsd:string +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role [Typedef] id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic [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: editor_note "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: example_of_usage "this apple has quality this red color" xsd:string +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 range: BFO:0000019 ! quality -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "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." xsd:string -property_value: example_of_usage "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "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." xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000091 @@ -1022,7 +843,7 @@ name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition -is_a: has_characteristic ! has_characteristic +is_a: RO:0000053 ! has characteristic inverse_of: RO:0000092 ! disposition of [Typedef] @@ -1031,7 +852,7 @@ name: disposition of def: "inverse of has disposition" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. subset: RO:0002259 -is_a: characteristic_of ! characteristic_of +is_a: RO:0000052 ! characteristic of [Typedef] id: RO:0002013 @@ -1157,40 +978,55 @@ property_value: IAO:0000118 "meets" xsd:string 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: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: RO:0001900 RO:0001901 +holds_over_chain: BFO:0000050 BFO:0000050 +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} +holds_over_chain: BFO:0000051 RO:0002131 +is_symmetric: true +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: editor_note "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: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: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002206 name: expressed in def: "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" [] -property_value: example_of_usage "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string +property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant -range: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 is_a: RO:0002330 ! genomically related to -inverse_of: expresses ! expresses -transitive_over: part_of ! part_of +inverse_of: RO:0002292 ! expresses +transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002211 name: regulates -namespace: gene_ontology def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002211 property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 @@ -1210,12 +1046,10 @@ transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 name: negatively regulates -namespace: gene_ontology def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002212 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string @@ -1227,12 +1061,10 @@ inverse_of: RO:0002335 ! negatively regulated by [Typedef] id: RO:0002213 name: positively regulates -namespace: gene_ontology def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002213 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -1243,6 +1075,33 @@ 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 https://orcid.org/0000-0002-6601-2165 +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 +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of + +[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 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + [Typedef] id: RO:0002222 name: temporally related to @@ -1277,7 +1136,7 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: example_of_usage "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: 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: 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 @@ -1288,11 +1147,19 @@ 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." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: example_of_usage "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: 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: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002292 +name: expresses +def: "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002330 ! genomically related to + [Typedef] id: RO:0002304 name: causally upstream of, positive effect @@ -1322,15 +1189,15 @@ is_a: RO:0004046 ! causally upstream of or within, negative effect id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: characteristic_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002323 @@ -1345,7 +1212,7 @@ id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string @@ -1354,9 +1221,9 @@ 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: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI -is_a: capable_of ! capable_of +is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by -transitive_over: has_part ! has part +transitive_over: BFO:0000051 ! has part transitive_over: RO:0002017 ! has component activity [Typedef] @@ -1372,7 +1239,7 @@ 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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -1392,10 +1259,10 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI -holds_over_chain: RO:0002327 part_of +holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002333 @@ -1439,12 +1306,12 @@ is_a: RO:0002334 ! regulated by id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: example_of_usage "An organism that is a member of a population of organisms" xsd:string +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: RO:0001900 RO:0001901 -is_a: part_of ! part_of +is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] @@ -1453,7 +1320,7 @@ 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: RO:0001900 RO:0001901 -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002352 @@ -1519,7 +1386,7 @@ transitive_over: RO:0002630 ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 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 @@ -1548,7 +1415,7 @@ id: RO:0002418 name: causally upstream of or within def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true @@ -1599,7 +1466,7 @@ is_a: RO:0002428 ! involved in regulation of 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: editor_note "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -1613,8 +1480,8 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 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: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI @@ -1637,7 +1504,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 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 is_a: RO:0002436 ! molecularly interacts with @@ -1718,7 +1585,7 @@ property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 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 @@ -1779,9 +1646,9 @@ is_a: RO:0002412 ! immediately causally upstream of 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: example_of_usage "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: has_part capable_of +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 @@ -1789,7 +1656,7 @@ is_a: RO:0002595 ! causal relation between material entity and a process 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: editor_note "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: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 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity @@ -1800,9 +1667,9 @@ is_a: RO:0002410 ! causally related to 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: example_of_usage "pyrethroid -> growth" xsd:string +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -holds_over_chain: capable_of RO:0002211 +holds_over_chain: RO:0002215 RO:0002211 is_a: RO:0002500 ! causal agent in process [Typedef] @@ -1810,16 +1677,16 @@ 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 -holds_over_chain: capable_of RO:0002212 +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: example_of_usage "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -holds_over_chain: capable_of RO:0002213 +holds_over_chain: RO:0002215 RO:0002213 is_a: RO:0002596 ! capable of regulating [Typedef] @@ -1829,12 +1696,6 @@ def: "Inverse of 'causal agent in process'" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to -[Typedef] -id: RO:0002610 -name: correlated with -def: "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." [] -property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string - [Typedef] id: RO:0002629 name: directly positively regulates @@ -1863,11 +1724,22 @@ property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regul is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates +[Typedef] +id: RO:0004028 +name: realized in response to stimulus +def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] +domain: BFO:0000017 ! realizable entity +range: BFO:0000040 ! material entity +holds_over_chain: RO:0009501 RO:0002233 +is_a: RO:0002410 ! causally related to +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-12-26T19:45:49Z + [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." [] -holds_over_chain: RO:0002327 has_part +holds_over_chain: RO:0002327 BFO:0000051 is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -1938,6 +1810,52 @@ is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z +[Typedef] +id: RO:0009501 +name: realized in response to +def: "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." [] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 +property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string +property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +holds_over_chain: BFO:0000054 RO:0002404 +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0010001 +name: generically depends on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string +property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string +property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string +property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string +property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0000052 RO:0000058 +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is carrier of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string +property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string +property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000031 ! generically dependent continuant +holds_over_chain: RO:0000059 RO:0000053 + [Typedef] id: RO:0011002 name: regulates activity of @@ -1969,31 +1887,21 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: example_of_usage "A diagnostic testing device utilizes a specimen." xsd:string +property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string -holds_over_chain: capable_of RO:0002233 +holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z -[Typedef] -id: RO:0017003 -name: positively correlated with -def: "A relation between entities in which one increases or decreases as the other does the same." [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 -property_value: IAO:0000118 "directly correlated with" xsd:string -is_reflexive: true -is_symmetric: true -is_a: RO:0002610 ! correlated with - [Typedef] id: RO:0019000 name: regulates characteristic def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process -range: PATO:0000001 ! quality +range: PATO:0000001 holds_over_chain: RO:0002211 RO:0019000 is_a: RO:0002410 ! causally related to @@ -2041,125 +1949,10 @@ id: VFBext:0000009 name: has driver def: "A relation that applies between a synthetic expression pattern and a transgene that drives it. For example, the GAL4 UAS system uses the yeast transcription factor GAL4 transgenes with specific expression patterns are used to drive expression of transgenes under the control of UAS promoter elements." [PMID:8223268, Wikipedia:GAL4/UAS_system] domain: CARO:0030002 ! expression pattern -is_a: expresses ! expresses +is_a: RO:0002292 ! expresses created_by: dos creation_date: 2018-09-26T07:49:10Z -[Typedef] -id: capable_of -name: capable of -name: capable_of -namespace: fly_anatomy.ontology -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 -xref: RO:0002215 -property_value: example_of_usage "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: example_of_usage "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -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 -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: capable_of_part_of ! capable_of_part_of - -[Typedef] -id: capable_of_part_of -name: capable of part of -name: capable_of_part_of -namespace: fly_anatomy.ontology -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." [] -xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: characteristic_of -name: characteristic of -name: characteristic_of -namespace: fly_anatomy.ontology -def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] -comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -xref: RO:0000052 -property_value: example_of_usage "this fragility is a characteristic of this vase" xsd:string -property_value: example_of_usage "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 -is_functional: true -is_a: RO:0002314 ! characteristic of part of -inverse_of: has_characteristic ! has_characteristic - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -xref: IAO:0000116 -is_metadata_tag: true - -[Typedef] -id: example_of_usage -name: example of usage -namespace: uberon -xref: IAO:0000112 -is_metadata_tag: true - -[Typedef] -id: expresses -name: expresses -namespace: fly_anatomy.ontology -def: "y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -xref: RO:0002292 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: has_characteristic -name: has characteristic -name: has_characteristic -namespace: fly_anatomy.ontology -def: "Inverse of characteristic_of" [] -xref: RO:0000053 -property_value: editor_note "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: example_of_usage "this apple is bearer of this red color" xsd:string -property_value: example_of_usage "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant -is_inverse_functional: true - -[Typedef] -id: has_part -name: has part -name: has_part -namespace: quality -namespace: relationship -def: "a core relation that holds between a whole and its part" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000051 -xref: OBO_REL:has_part -property_value: editor_note "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: editor_note "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "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: example_of_usage "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: example_of_usage "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: example_of_usage "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: overlaps ! overlaps - [Typedef] id: http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7 name: has_exemplar @@ -2173,59 +1966,3 @@ is_a: RO:0002350 ! member of id: http://xmlns.com/foaf/0.1/depicts name: depicts -[Typedef] -id: overlaps -name: overlaps -namespace: fly_anatomy.ontology -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_gocam -subset: ro-eco -xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: part_of part_of -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of -expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] - -[Typedef] -id: part_of -name: part of -name: part_of -namespace: quality -namespace: relationship -def: "a core relation that holds between a part and its whole" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: BFO:0000050 -xref: OBO_REL:part_of -property_value: editor_note "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: editor_note "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "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: example_of_usage "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: example_of_usage "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: example_of_usage "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -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 -property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI -is_transitive: true -is_a: overlaps ! overlaps -inverse_of: has_part ! has part - diff --git a/vfbext.owl b/vfbext.owl index b70521e..726dc13 100644 --- a/vfbext.owl +++ b/vfbext.owl @@ -2,7 +2,6 @@ + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology https://creativecommons.org/licenses/by/4.0/</terms:license> - 15:08:2023 10:37 + 26:10:2023 13:58 VFB extension ontology - 2023-08-15 + 2023-10-26 @@ -47,24 +42,6 @@ - - - - - - - - - - - - - - - - - - @@ -73,14 +50,7 @@ - - IAO:0000112 - uberon - example_of_usage - true - example_of_usage - example of usage - + @@ -93,47 +63,14 @@ - 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 - - IAO:0000116 - uberon - editor_note - true - editor_note - editor note - + @@ -167,6 +104,12 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + + + @@ -185,27 +128,9 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - + - - - - - - - - - - - - - + @@ -215,12 +140,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -317,17 +236,19 @@ We also have the outstanding issue of how to aim different definitions to differ - + - + - + - + + + @@ -395,188 +316,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -585,67 +324,27 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - + - + @@ -717,12 +416,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -741,12 +434,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -773,23 +460,9 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - has_obo_namespace - + @@ -799,12 +472,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - @@ -819,36 +486,12 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - @@ -870,7 +513,7 @@ We also have the outstanding issue of how to aim different definitions to differ @@ -878,24 +521,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - + @@ -920,18 +546,11 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - BFO:0000050 - OBO_REL:part_of - quality - relationship - part_of - part_of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -957,30 +576,48 @@ 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 - BFO:0000051 - OBO_REL:has_part - quality - relationship - has_part - has_part 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 + @@ -1001,7 +638,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1035,12 +672,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - @@ -1050,7 +681,17 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has_specified_input + has_specified_input + see is_input_of example_of_usage + The inverse property of is_specified_input_of + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot + has_specified_input @@ -1060,7 +701,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. + is_specified_input_of + some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters is_specified_input_of @@ -1075,7 +721,15 @@ A continuant cannot have an occurrent as part: use 'participates in'. + has_specified_output + has_specified_output + The inverse property of is_specified_output_of + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot + has_specified_output @@ -1085,7 +739,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. + is_specified_output_of + is_specified_output_of + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + Alan Ruttenberg + PERSON:Bjoern Peters + is_specified_output_of @@ -1094,21 +754,18 @@ A continuant cannot have an occurrent as part: use 'participates in'. + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective - - - - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. - objective_achieved_by - - - - @@ -1121,13 +778,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in - RO:0000052 - fly_anatomy.ontology - characteristic_of - characteristic_of Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of - characteristic_of @@ -1145,12 +797,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. bearer_of is bearer of - RO:0000053 - fly_anatomy.ontology - has_characteristic - has_characteristic has characteristic - has_characteristic @@ -1177,6 +824,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + @@ -1188,15 +840,36 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + 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 + @@ -1563,14 +1236,9 @@ Examples include: the relationship between two channels collected simultaneously 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) - RO:0002131 - fly_anatomy.ontology - overlaps - overlaps - overlaps overlaps @@ -1654,9 +1322,6 @@ Examples include: the relationship between two channels collected simultaneously Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false - RO:0002211 - gene_ontology - regulates @@ -1676,9 +1341,6 @@ Examples include: the relationship between two channels collected simultaneously negatively regulates (process to process) - RO:0002212 - gene_ontology - negatively_regulates @@ -1703,9 +1365,6 @@ Examples include: the relationship between two channels collected simultaneously positively regulates (process to process) - RO:0002213 - gene_ontology - positively_regulates @@ -1728,13 +1387,8 @@ Examples include: the relationship between two channels collected simultaneously 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:0002215 - fly_anatomy.ontology - capable_of - capable_of capable of - capable_of @@ -1751,12 +1405,7 @@ Examples include: the relationship between two channels collected simultaneously 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. has function in - RO:0002216 - fly_anatomy.ontology - capable_of_part_of - capable_of_part_of capable of part of - capable_of_part_of @@ -1850,11 +1499,6 @@ Examples include: the relationship between two channels collected simultaneously y expresses x 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 x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - RO:0002292 - fly_anatomy.ontology - expresses - expresses - expresses expresses @@ -2744,16 +2388,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - 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 - - - - @@ -2790,6 +2424,24 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. + + 2017-12-26T19:45:49Z + realized in response to stimulus + + + + @@ -2908,6 +2560,79 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. + An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) + 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. + + + + + triggered by process + realized in response to + https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit + + + + + triggered by process + + + + + + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + @@ -2959,27 +2684,13 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material - - - - - - - A relation between entities in which one increases or decreases as the other does the same. - directly correlated with - - positively correlated with - - - - @@ -3123,43 +2834,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - 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]) - - - - - - @@ -3173,76 +2850,9 @@ For example, A and B may be gene products and binding of B by A positively regul - continuant - Continuant 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. - 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 - - - - 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] - - @@ -3279,65 +2889,10 @@ For example, A and B may be gene products and binding of B by A positively regul - 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 - 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]) - 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] 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 - - - - 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] - - @@ -3484,10 +3039,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. CARO:0000000 Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. @@ -3502,6 +3053,60 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + + Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. + connected anatomical structure + + + + + + + + + Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle. + Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome. + portion of organism substance + CARO:0000004 + Note - CARO explicitly declares organisms substances to be part of (some) organism. + organism substance + + + + @@ -3572,1286 +3177,758 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - An anatomical structure consisting of one or more cells. - - 2018-09-28T14:20:19Z - cellular anatomical structure + + + Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. + CARO:0000012 + MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + +MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. + multicellular organism - + - - - Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. - Important for alignment with Darwin Core class "Organism". - biological entity + + + + + + + + + An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CL:0000000 + GO:0005623 + CARO:0000013 + deprecate and replace with CL or GO term? + cell - + - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. - expression pattern + + + + + + + + + + + + + Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher. + cell component + CARO:0000014 + This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class. + cell part - + - - - Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. - CARO:0000003 - UBERON:0000061 - fly_anatomy.ontology - FBbt:00007001 - - - anatomical structure + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism. + CARO:0000032 + + organism subdivision - - - - Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. - CARO:MAH - FBC:DOS - - + - - - CARO:0000006 - UBERON:0000465 - fly_anatomy.ontology - FBbt:00007016 - - - material anatomical entity + + + + + + + + 0 + + + + + 0 + + + + + + + + + + + An anatomical structure that has no cells or cell parts as a part. + CARO:0000040 + Example. Insect cuticle, eggshell, hair. + acellular anatomical structure - + - - - Anatomical structure that has multiple cells as parts. - - 2010-11-02T02:25:04Z - UBERON:0010000 - fly_anatomy.ontology - FBbt:00100313 - multicellular structure + + + + + + A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. + CARO:0000042 + + MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids? + + extraembryonic structure - - - - Anatomical structure that has multiple cells as parts. - FBC:DOS - - + - - + + + - + - - + + + + + + + + + + 2 + - - - - - - - - - Anatomical entity which is part_of Drosophila melanogaster. - FBbt_root:00000000 - UBERON:0001062 - fly_anatomy.ontology - Drosophila - FBbt:10000000 - - - - anatomical entity + + A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. + multi-cell-component structure + CARO:0001000 + + Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain. + multi-cell-part structure - - - - Anatomical entity which is part_of Drosophila melanogaster. - CARO:MAH - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GO:0005554 - molecular function - molecular_function - GO:0003674 - - - - - - - Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. - molecular_function - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GOC:pdt - - - + - - - - - Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. - Wikipedia:Enzyme - enzyme activity - molecular_function - GO:0003824 - - - - - - - - catalytic activity + + + + + + + + + + + + + + + + + + + + + Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. + + 10.7.2011 + + gross anatomical part - - - - Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. - GOC:vw - ISBN:0198506732 - - - - - enzyme activity - GOC:dph - GOC:tb - - + - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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. - https://github.com/geneontology/go-ontology/issues/24968 - jl - 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 + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + Melissa Haendel + 9/18/11 + organism or virus or viroid + organism - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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 - - + - - + + + + - - true + + - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - Reactome:R-HSA-6788855 - Reactome:R-HSA-6788867 - phosphokinase activity - molecular_function - GO:0016301 - - - - - - Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. - kinase activity + An anatomical structure that has more than one cell as a part. + djs93 + Sun Feb 27 10:53:00 GMT 2011 + CARO:0010000 + + multicellular anatomical structure - - - - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - ISBN:0198506732 - - - - - Reactome:R-HSA-6788855 - FN3KRP phosphorylates PsiAm, RibAm - - - - - Reactome:R-HSA-6788867 - FN3K phosphorylates ketosamines - - - - - - - - - Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. - EC:2.-.-.- - Reactome:R-HSA-1483089 - Reactome:R-HSA-1483186 - Reactome:R-HSA-5668414 - Reactome:R-HSA-8868783 - molecular_function - GO:0016740 - - - - - - - - - - - transferase activity + + + + + + + + - - - Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. - ISBN:0198506732 - - - - - Reactome:R-HSA-1483089 - PE is converted to PS by PTDSS2 - - - - - Reactome:R-HSA-1483186 - PC is converted to PS by PTDSS1 - - - - - Reactome:R-HSA-5668414 - TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK - - - - - Reactome:R-HSA-8868783 - TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 + + + + There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS - + - - - Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). - EC:2.7.-.- - molecular_function - GO:0016772 - - Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. - transferase activity, transferring phosphorus-containing groups + + + + An individual member of a clade of cellular organisms. + + 7.16.2011 + CARO:0010004 + 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. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + cellular organism - - - - Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). - GOC:jl - ISBN:0198506732 - - + - + - - - - - - - - - - - + + + + + + + + + 2 + + + - 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 - - - - - - - - GC_ID:1 - ncbi_taxonomy - all - NCBITaxon:1 - root - - - - - all - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:1206794 - Ecdysozoa - - - - - - - - - GC_ID:1 - ncbi_taxonomy - biota - NCBITaxon:131567 - cellular organisms - - - - - biota - - - - - - - - - - - GC_ID:1 - PMID:10874751 - PMID:11557979 - ncbi_taxonomy - NCBITaxon:197562 - Pancrustacea + + + + + + + + + + + + + + Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. + CARO:0000054 + + disconnected anatomical group - + - - - - GC_ID:1 - PMID:11557979 - PMID:9727836 - mandibulates - ncbi_taxonomy - NCBITaxon:197563 - Mandibulata + + + + An anatomical structure consisting of one or more cells. + + 2018-09-28T14:20:19Z + cellular anatomical structure - - - - mandibulates - - - - - - - - - - - GC_ID:1 - PMID:23020233 - PMID:30257078 - eucaryotes - eukaryotes - ncbi_taxonomy - Eucarya - Eucaryotae - Eukarya - Eukaryotae - eukaryotes - NCBITaxon:2759 - Eukaryota + + + + + + + + - - - eucaryotes - - - - - - eukaryotes - - - - - - Eucarya - - - - - - Eucaryotae - - - - - - Eukarya - - - - - - Eukaryotae - - - - - - eukaryotes - + + + + With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32341 - Sophophora - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32346 - melanogaster group - - - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32351 - melanogaster subgroup + + + Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them. + Important for alignment with Darwin Core class "Organism". + biological entity - + - - - - GC_ID:1 - ncbi_taxonomy - Fungi/Metazoa group - opisthokonts - NCBITaxon:33154 - Opisthokonta + + + + + + + + + The mereological sum of all cells in a single organism in which expression of some specified gene occurs. + expression pattern - - - - Fungi/Metazoa group - - - - - - opisthokonts - - - + - - - - GC_ID:1 - metazoans - multicellular animals - ncbi_taxonomy - Animalia - animals - NCBITaxon:33208 - Metazoa + + + Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. + CARO:0000003 + UBERON:0000061 + fly_anatomy.ontology + FBbt:00007001 + + + anatomical structure - - - metazoans - - - - - - multicellular animals - - - - - - Animalia - - - - - - animals - + + + Material anatomical entity that has inherent 3D shape, whose parts are all connected and that is generated by coordinated expression of the organism's own genome. + https://orcid.org/0000-0001-9114-8737 + https://orcid.org/0000-0002-7073-9172 - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33213 - Bilateria - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33317 - Protostomia - - - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33340 - Neoptera + + + CARO:0000006 + UBERON:0000465 + fly_anatomy.ontology + FBbt:00007016 + + + material anatomical entity - + - - - - GC_ID:1 - ncbi_taxonomy - Holometabola - NCBITaxon:33392 - Endopterygota + + + Anatomical structure that has multiple cells as parts. + + 2010-11-02T02:25:04Z + UBERON:0010000 + fly_anatomy.ontology + FBbt:00100313 + multicellular structure - - - Holometabola - + + + Anatomical structure that has multiple cells as parts. + https://orcid.org/0000-0002-7073-9172 - + - - - - NCBITaxon:43732 - GC_ID:1 - ncbi_taxonomy - Asilomorpha - NCBITaxon:43733 - Muscomorpha + + + + + + + + + + + + + + + + + + + + + Anatomical entity which is part_of Drosophila melanogaster. + FBbt_root:00000000 + UBERON:0001062 + fly_anatomy.ontology + Drosophila + FBbt:10000000 + + + + anatomical entity - - - Asilomorpha - + + + Anatomical entity which is part_of Drosophila melanogaster. + https://orcid.org/0000-0001-9114-8737 - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43738 - Schizophora - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43741 - Acalyptratae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43746 - Ephydroidea - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:43845 - Drosophilinae - - - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:46877 - Drosophilini - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:480117 - Cyclorrhapha + + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:480118 - Eremoneura + + + + + true + + - + - - - - GC_ID:1 - true insects - ncbi_taxonomy - insects - NCBITaxon:50557 - Insecta - - - - - true insects - - - - - - insects - - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:6072 - Eumetazoa - + - + - - - - GC_ID:1 - arthropods - ncbi_taxonomy - arthropods - NCBITaxon:6656 - Arthropoda - - - - - arthropods - - - - - - arthropods - - + - + - - - - GC_ID:1 - insects - ncbi_taxonomy - Atelocerata - Tracheata - Uniramia - hexapods - NCBITaxon:6960 - Hexapoda + + + + + + + + + + + + + + + + + + + + + + + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy + + A process that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + planned process - - - - insects - - - - - - Atelocerata - - - - - - Tracheata - - - - - - Uniramia - - - - - - hexapods - - - + - - - - GC_ID:1 - flies - ncbi_taxonomy - flies - NCBITaxon:7147 - Diptera + + + + + + + + + + + + + + + + + + + specimen role + liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. + + a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen. + parasite example +- when parasite in people we study people, people are subjects and parasites are specimen +- when parasite extracted, they become subject in the following study +specimen can later be subject. + GROUP: Role Branch + OBI + + specimen role - - - - flies - - - - - - flies - - - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:7203 - Brachycera + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specimen collection process + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + + A planned process with the objective of collecting a specimen. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. + Philly2013: The specimen_role for the specimen is created during the specimen collection process. + label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/ + Bjoern Peters + specimen collection + 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession + 6/9/09: used at workshop + specimen collection process - + - - - - GC_ID:1 - pomace flies - ncbi_taxonomy - NCBITaxon:7214 - Drosophilidae + + + specimen collection objective + The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. + + A objective specification to obtain a material entity for potential use as an input during an investigation. + Bjoern Peters + Bjoern Peters + specimen collection objective - - - - pomace flies - - - + - - - - NCBITaxon:7326 - GC_ID:1 - Drosophila - fruit flies - fruit fly - ncbi_taxonomy - NCBITaxon:7215 - Drosophila <flies,genus> + + + + + + + + + + + + + + collection of specimens + Blood cells collected from multiple donors over the course of a study. + + A material entity that has two or more specimens as its parts. + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Person: Chris Stoeckert, Jie Zheng + OBIB, OBI + Biobank + collection of specimens - - - - Drosophila - - - - - - fruit flies - - - - - - fruit fly - - - + - - - - NCBITaxon:2267365 - GC_ID:1 - fruit fly - ncbi_taxonomy - Sophophora melanogaster - NCBITaxon:7227 - Drosophila melanogaster + + + + + + + + + + + + + + + + + + + + specimen + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + + A material entity that has the specimen role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch + + specimen - - - - fruit fly - - - - - - Sophophora melanogaster - - - + - - - - GC_ID:1 - Pterygota - winged insects - ncbi_taxonomy - NCBITaxon:7496 - Pterygota <insects> - - - - - Pterygota - - - - - - winged insects - - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:85512 - Dicondylia - + - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:88770 - Panarthropoda - + - + - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - 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 dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. - PATOC:GVG - + - + - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - quality - PATO:0000125 - - - - For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. - mass - - - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - PATOC:GVG - + - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - PATO:0002079 - Wikipedia:Physical_property - relational physical quality - quality - PATO:0001018 - - 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 a continuant. - PATO:0001237 - PATO:0001238 - snap:Quality - monadic quality of a continuant - multiply inhering quality of a physical entity - 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 - + - + - + - - Anatomical entity that has mass. - - - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FBbt:00007016 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - UBERON:0000465 - - - material anatomical entity - - - - Anatomical entity that has mass. - http://orcid.org/0000-0001-9114-8737 - - + - - - 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. - - - AAO:0010841 - AEO:0000000 - BILA:0000000 - BIRNLEX:6 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FMA:62955 - HAO:0000000 - MA:0000001 - NCIT:C12219 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - WBbt:0000100 - XAO:0000000 - ZFA:0100000 - UBERON:0001062 - - - anatomical entity - - - - - 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. - FMA:62955 - http://orcid.org/0000-0001-9114-8737 - - - - - UMLS:C1515976 - ncithesaurus:Anatomic_Structure_System_or_Substance - + @@ -4940,115 +4017,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - metadata complete - 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 - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - ready for release - - 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 - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - - 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 - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - - 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 - - - - - - - - - - - - - - - - - - - - Should belong in BFO, but lives in caro for now. - - - - - @@ -5112,17 +4059,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - + + + + + + @@ -5141,10 +4083,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + @@ -5189,15 +4131,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -5207,15 +4149,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -5281,10 +4223,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5292,9 +4233,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5324,10 +4266,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5335,9 +4276,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5367,10 +4309,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5378,9 +4319,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5410,10 +4352,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - + + + @@ -5421,9 +4362,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + @@ -5888,9 +4830,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -5899,9 +4841,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -5933,9 +4875,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -5944,9 +4886,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -5978,9 +4920,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -5989,9 +4931,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6023,9 +4965,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6034,9 +4976,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6068,9 +5010,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6079,9 +5021,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -6113,7 +5055,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6124,7 +5066,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6141,7 +5083,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6151,7 +5093,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6169,7 +5111,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6180,7 +5122,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6197,7 +5139,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6207,7 +5149,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6224,7 +5166,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6235,7 +5177,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -6268,9 +5210,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6279,9 +5221,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6312,9 +5254,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6323,9 +5265,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6356,9 +5298,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6367,9 +5309,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6400,9 +5342,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6411,9 +5353,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -6445,8 +5387,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -6456,8 +5398,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -6484,5 +5426,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - +