diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..ce2a2dc --- /dev/null +++ b/LICENSE.md @@ -0,0 +1 @@ +Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License. \ No newline at end of file diff --git a/imports/caro_import.owl b/imports/caro_import.owl index 77ff448..ec05a7b 100644 --- a/imports/caro_import.owl +++ b/imports/caro_import.owl @@ -7,17 +7,19 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:caro="http://purl.obolibrary.org/obo/caro#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> - - - 2022-01-24 + + None + + Common Anatomy Reference Ontology + + Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendal. + 2022-02-18 + 2022-02-25 @@ -45,21 +47,18 @@ - - - - - - - - - - - - - + + IAO:0000112 + uberon + example_of_usage + true + example_of_usage + + example of usage + example of usage + @@ -75,43 +74,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + editor note + - + + + elucidation + @@ -133,52 +114,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -187,27 +122,15 @@ - - database_cross_reference - - - - - - - - - - - - - + - + + has_obo_namespace + @@ -225,290 +148,39 @@ - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - - has part - - - - - - - - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple - 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 - - 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 - - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - has characteristic - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - 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. - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - 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. - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - 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. - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - + - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - + - + - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - + - - - - - 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. - disposition of - - - + - - - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - overlaps - + - + - - - - For use in recording has_part with a cardinality constraint. - Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ? - has component - + - + - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - + - + - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - + @@ -526,6 +198,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + entity Entity Julius Caesar @@ -575,6 +248,24 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + + @@ -611,24 +302,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. (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 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 - - @@ -636,8 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - ic IndependentContinuant a chair @@ -699,393 +370,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - 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. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - 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. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - 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. @@ -1100,69 +388,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - An anatomical entity that has mass. CARO:0000006 @@ -1171,362 +400,15 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - - - - - - - - - - - - - Anatomical entity that has no mass. - CARO:0000007 - - immaterial anatomical entity - - - - - - - - - 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 - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 - - - - - - - - - - - - - - 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 - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - 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 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. - mah - 10.7.2011 - - gross anatomical part - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - An individual member of a clade of cellular organisms. - mah - 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 - - - - - - - - - - - - - - - - - - 2 - - - - - - Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. - CARO:0000054 - - disconnected anatomical group - - - - - - - - - - - - - - - An anatomical structure consisting of one or more cells. 2018-09-28T14:20:19Z cellular anatomical structure dos - - - - - - - - - - - - - - - With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell - @@ -1545,460 +427,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. expression pattern - - - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - - - - - - Viruses - - - - - - - - - Viroids - - - - - - - - - cellular organisms - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. - trait - quality - PATO:0000001 - quality - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. - PATOC:GVG - - - - - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - quality - PATO:0000051 - morphology - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - PATOC:GVG - - - - - - - - - shape - - - - - - - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - PATO:0000125 - mass - - - - - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - relational structural quality - quality - PATO:0000141 - structure - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATOC:GVG - - - - - - - - - physical quality - - - - - - - - - A quality which inheres in a continuant. - monadic quality of a continuant - multiply inhering quality of a physical entity - quality of a continuant - quality of a single physical entity - quality of an object - quality of continuant - monadic quality of an object - monadic quality of continuant - quality - PATO:0001241 - physical object quality - - - - - A quality which inheres in a continuant. - PATOC:GVG - - - - - - - - - cellularity - - - - - - - - - multicellular - - - - - - - - - organismal quality - - - - - - - - - 3-D shape - - - - - - - - - maximally connected - - - - - - - - - disconnected - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Should belong in BFO, but lives in caro for now. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/imports/fbbt_import.owl b/imports/fbbt_import.owl index 99d2125..b67178f 100644 --- a/imports/fbbt_import.owl +++ b/imports/fbbt_import.owl @@ -18,9 +18,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2022-01-24 + + + 2022-02-25 @@ -301,24 +301,12 @@ - - - - - - - - - - - - @@ -331,12 +319,6 @@ - - - - - - @@ -2536,7 +2518,7 @@ For example, A and B may be gene products and binding of B by A positively regul 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 + CARO:MAH FBC:DOS @@ -2615,7 +2597,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity which is part_of Drosophila melanogaster. - CARO:MAH + CARO:MAH diff --git a/imports/obi_import.owl b/imports/obi_import.owl index 0a20319..e650d8d 100644 --- a/imports/obi_import.owl +++ b/imports/obi_import.owl @@ -8,8 +8,8 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - - 2022-01-24 + + 2022-02-25 diff --git a/imports/ro_import.owl b/imports/ro_import.owl index abf2eca..9f9d2eb 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -16,9 +16,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2022-01-24 + + + 2022-02-25 diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 258f479..5abd0af 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for vfbext # Generated using ontology-development-kit -# ODK Version: v1.2.32 +# ODK Version: v1.3.0 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vfbext.Makefile instead @@ -28,6 +28,9 @@ RELEASEDIR= ../.. REPORTDIR= reports TEMPLATEDIR= ../templates TMPDIR= tmp +MIRRORDIR= mirror +IMPORTDIR= imports +SUBSETDIR= subsets SCRIPTSDIR= ../scripts SPARQLDIR = ../sparql COMPONENTSDIR = components @@ -35,9 +38,9 @@ REPORT_FAIL_ON = None REPORT_LABEL = -l true REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = -SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference -SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.2.32 +SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri +SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms +ODK_VERSION_MAKEFILE = v1.3.0 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -57,10 +60,10 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-simple $(ONT)-non-classified $(ONT .PHONY: .FORCE .PHONY: all -all: odkversion all_imports all_main all_subsets sparql_test all_reports all_assets +all: odkversion test all_assets .PHONY: test -test: odkversion sparql_test all_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt +test: odkversion sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt $(ROBOT) reason --input $(SRC) --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural --output test.owl && rm test.owl && echo "Success" .PHONY: odkversion @@ -68,28 +71,29 @@ odkversion: echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, not the version of the ODK you are running)" &&\ echo "ROBOT version (ODK): " && $(ROBOT) --version -$(TMPDIR) $(REPORTDIR) : +$(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR): mkdir -p $@ -## -- main targets -- -## -## By default this is the cross-product of {ont, ont-base} x FORMATS +# ---------------------------------------- +# Release assets +# ---------------------------------------- MAIN_PRODUCTS = $(sort $(foreach r,$(RELEASE_ARTEFACTS), $(r)) $(ONT)) -MAIN_GZIPPED = -MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED) +MAIN_GZIPPED = +MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED) +SRCMERGED = $(TMPDIR)/merged-$(SRC) .PHONY: all_main all_main: $(MAIN_FILES) -## -- import targets -- -## -## By default this is the cross-product of IMPORT_MODULES x FORMATS +# ---------------------------------------- +# Import assets +# ---------------------------------------- IMPORTS = ro caro fbbt obi -IMPORT_ROOTS = $(patsubst %, imports/%_import, $(IMPORTS)) +IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) IMPORT_FILES = $(IMPORT_OWL_FILES) @@ -97,20 +101,23 @@ IMPORT_FILES = $(IMPORT_OWL_FILES) .PHONY: all_imports all_imports: $(IMPORT_FILES) -## -- subset targets -- -## -## By default this is the cross-product of SUBSETS x FORMATS -## Note we also include TSV as a format +# ---------------------------------------- +# Subset assets +# ---------------------------------------- SUBSETS = -SUBSET_ROOTS = $(patsubst %, subsets/%, $(SUBSETS)) +SUBSET_ROOTS = $(patsubst %, $(SUBSETDIR)/%, $(SUBSETS)) SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f))) .PHONY: all_subsets all_subsets: $(SUBSET_FILES) +# ---------------------------------------- +# QC Reports & Utilities +# ---------------------------------------- + OBO_REPORT = $(SRC)-obo-report REPORTS = $(OBO_REPORT) REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS)) @@ -119,16 +126,48 @@ REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS)) robot_reports: $(REPORT_FILES) .PHONY: all_reports -all_reports: all_reports_onestep $(REPORT_FILES) +all_reports: custom_reports robot_reports + +# ---------------------------------------- +# ROBOT OWL Profile checking +# ---------------------------------------- -$(REPORTDIR)/validate_profile_owl2dl_%.txt: % | $(REPORTDIR) - $(ROBOT) validate-profile --profile DL -i $< -o $@ +# The conversion to functional syntax is necessary to avoid undeclared entity violations. +$(REPORTDIR)/validate_profile_owl2dl_%.txt: % | $(REPORTDIR) $(TMPDIR) + $(ROBOT) merge -i $< convert -f ofn -o $(TMPDIR)/validate.ofn + $(ROBOT) validate-profile --profile DL -i $(TMPDIR)/validate.ofn -o $@ || { cat $@ && exit 1; } .PRECIOUS: $(REPORTDIR)/validate_profile_owl2dl_%.txt -.PHONY: validate_profile_% validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt + echo "$* profile validation completed." + +# ---------------------------------------- +# Sparql queries: Q/C +# ---------------------------------------- -## -- all files/assets -- +# these live in the ../sparql directory, and have suffix -violation.sparql +# adding the name here will make the violation check live. + +SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) + +sparql_test: $(SRC) catalog-v001.xml | $(REPORTDIR) +ifneq ($(SPARQL_VALIDATION_QUERIES),) + $(ROBOT) verify --catalog catalog-v001.xml -i $< --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) +endif + +# ---------------------------------------- +# ROBOT report +# ---------------------------------------- + +$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR) + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@ + +$(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR) + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@ + +# ---------------------------------------- +# Release assets +# ---------------------------------------- ASSETS = \ $(IMPORT_FILES) \ @@ -143,13 +182,11 @@ RELEASE_ASSETS = \ .PHONY: all_assets all_assets: $(ASSETS) - .PHONY: show_assets show_assets: echo $(ASSETS) du -sh $(ASSETS) - # ---------------------------------------- # Release Management # ---------------------------------------- @@ -159,31 +196,26 @@ CLEANFILES=$(MAIN_FILES) $(SRCMERGED) # It will ensure that all assets/files are fresh, and will copy to release folder .PHONY: prepare_release -prepare_release: $(ASSETS) $(PATTERN_RELEASE_FILES) +prepare_release: all rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ - rm -f $(CLEANFILES) &&\ - 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" + rm -f $(CLEANFILES) &&\ + 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" .PHONY: prepare_initial_release -prepare_initial_release: prepare_release +prepare_initial_release: all_assets + rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ + rm -f $(patsubst %, ./%, $(CLEANFILES)) &&\ cd $(RELEASEDIR) && git add $(RELEASE_ASSETS) -# ---------------------------------------- -# Import modules -# ---------------------------------------- -# Most ontologies are modularly constructed using portions of other ontologies -# These live in the imports/ folder - # ------------------------ # Imports: Seeding system # ------------------------ # seed.txt contains all referenced entities IMPORTSEED=$(TMPDIR)/seed.txt -SRCMERGED=$(TMPDIR)/merged-$(SRC) PRESEED=$(TMPDIR)/pre_seed.txt -$(SRCMERGED): $(SRC) +$(SRCMERGED): $(SRC) $(OTHER_SRC) $(ROBOT) remove --input $< --select imports --trim false \ merge $(patsubst %, -i %, $(OTHER_SRC)) -o $@ @@ -203,41 +235,44 @@ $(SIMPLESEED): $(SRCMERGED) $(ONTOLOGYTERMS) ALLSEED = $(PRESEED) \ -$(IMPORTSEED): $(ALLSEED) +$(IMPORTSEED): $(ALLSEED) | $(TMPDIR) if [ $(IMP) = true ]; then cat $(ALLSEED) | sort | uniq > $@; fi - ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 -# -- Generate Import Modules -- -# +# ---------------------------------------- +# Import modules +# ---------------------------------------- +# Most ontologies are modularly constructed using portions of other ontologies +# These live in the imports/ folder # This pattern uses ROBOT to generate an import module -# Generate terms.txt for each import. (Assume OBO-style Possibly hacky step?) + # Should be able to drop this if robot can just take a big messy list of terms as input. -imports/%_terms_combined.txt: $(IMPORTSEED) imports/%_terms.txt +$(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi -imports/merged_import.owl: mirror/merged.owl imports/merged_terms_combined.txt - echo "ERROR: You have configured your default module type to be slme; this behavior needs to be overwritten in vfbext.Makefile!" && false - -imports/%_import.owl: mirror/%.owl imports/%_terms_combined.txt +$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ - extract -T imports/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \ + extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \ query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \ annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi -.PRECIOUS: imports/%_import.owl +.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 -imports/obi_import.owl: mirror/obi.owl imports/obi_terms_combined.txt - if [ $(IMP) = true ]; then $(ROBOT) extract -i $< -T imports/obi_terms_combined.txt --force true --method BOT \ +$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/obi_terms_combined.txt --force true --method BOT \ remove --base-iri $(URIBASE)/OBI --axioms external --preserve-structure false --trim false \ query --update ../sparql/inject-subset-declaration.ru \ - remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T imports/obi_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/obi_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi .PHONY: refresh-imports @@ -248,65 +283,59 @@ refresh-imports: no-mirror-refresh-imports: make IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B - .PHONY: refresh-imports-excluding-large refresh-imports-excluding-large: make IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B .PHONY: refresh-% refresh-%: - make IMP=true IMP_LARGE=true MIR=true PAT=false imports/$*_import.owl -B + make IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B .PHONY: no-mirror-refresh-% no-mirror-refresh-%: - make IMP=true IMP_LARGE=true MIR=false PAT=false imports/$*_import.owl -B - + make IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B # ---------------------------------------- # Mirroring upstream ontologies # ---------------------------------------- -# IMP=true # Global parameter to bypass import generation MIR=true # Global parameter to bypass mirror generation IMP_LARGE=true # Global parameter to bypass handling of large imports -## ONTOLOGY: ro -## Copy of ro is re-downloaded whenever source changes -mirror/ro.trigger: $(SRC) -mirror/ro.owl: mirror/ro.trigger - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ro.owl --create-dirs -o mirror/ro.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi -.PRECIOUS: mirror/ro.owl +## ONTOLOGY: ro +.PHONY: mirror-ro +.PRECIOUS: $(MIRRORDIR)/ro.owl +mirror-ro: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/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 ## ONTOLOGY: caro -## Copy of caro is re-downloaded whenever source changes -mirror/caro.trigger: $(SRC) - -mirror/caro.owl: mirror/caro.trigger - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/caro.owl --create-dirs -o mirror/caro.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/caro.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi -.PRECIOUS: mirror/caro.owl +.PHONY: mirror-caro +.PRECIOUS: $(MIRRORDIR)/caro.owl +mirror-caro: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/caro.owl --create-dirs -o $(MIRRORDIR)/caro.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: fbbt -## Copy of fbbt is re-downloaded whenever source changes -mirror/fbbt.trigger: $(SRC) - -mirror/fbbt.owl: mirror/fbbt.trigger - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/fbbt.owl --create-dirs -o mirror/fbbt.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/fbbt.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi -.PRECIOUS: mirror/fbbt.owl +.PHONY: mirror-fbbt +.PRECIOUS: $(MIRRORDIR)/fbbt.owl +mirror-fbbt: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/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 ## ONTOLOGY: obi -## Copy of obi is re-downloaded whenever source changes -mirror/obi.trigger: $(SRC) +.PHONY: mirror-obi +.PRECIOUS: $(MIRRORDIR)/obi.owl +mirror-obi: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + -mirror/obi.owl: mirror/obi.trigger - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/obi.owl --create-dirs -o mirror/obi.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/obi.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi -.PRECIOUS: mirror/obi.owl +$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) + if [ $(IMP) = true ] && [ $(MIR) = true ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." && cp $(TMPDIR)/mirror-$*.owl $@; fi; fi @@ -314,66 +343,33 @@ mirror/obi.owl: mirror/obi.trigger # ---------------------------------------- # Subsets # ---------------------------------------- -subsets/%.tsv: subsets/%.owl +$(SUBSETDIR)/%.tsv: $(SUBSETDIR)/%.owl $(ROBOT) query -f tsv -i $< -s ../sparql/labels.sparql $@ -.PRECIOUS: subsets/%.tsv +.PRECIOUS: $(SUBSETDIR)/%.tsv -subsets/%.owl: $(ONT).owl +$(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR) $(OWLTOOLS) $< --extract-ontology-subset --fill-gaps --subset $* -o $@.tmp.owl && mv $@.tmp.owl $@ &&\ $(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@.tmp.owl && mv $@.tmp.owl $@ -.PRECIOUS: subsets/%.owl +.PRECIOUS: $(SUBSETDIR)/%.owl -subsets/%.obo: subsets/%.owl +$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo -subsets/%.json: subsets/%.owl +$(SUBSETDIR)/%.json: $(SUBSETDIR)/%.owl $(ROBOT) convert --input $< --check false -f json -o $@.tmp.json &&\ jq -S 'walk(if type == "array" then sort else . end)' $@.tmp.json > $@ && rm $@.tmp.json -# ---------------------------------------- -# Release -# ---------------------------------------- -# copy from staging area (this directory) to top-level -.PHONY: release -release: $(ONT).owl $(ONT).obo - cp $^ $(RELEASEDIR) && cp imports/* $(RELEASEDIR)/imports - -# ---------------------------------------- -# Sparql queries: Q/C -# ---------------------------------------- - -# these live in the ../sparql directory, and have suffix -violation.sparql -# adding the name here will make the violation check live. -# NOTE: these will soon be phased out and replaced by robot-report - -# run all violation checks -SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) -sparql_test: $(SRC) catalog-v001.xml | $(REPORTDIR) -ifneq ($(SPARQL_VALIDATION_QUERIES),) - $(ROBOT) verify --catalog catalog-v001.xml -i $< --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) -endif - -# ---------------------------------------- -# ROBOT report -# ---------------------------------------- - -$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR) - $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@ - -$(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR) - $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@ - -# ---------------------------------------- -# Sparql queries: Exports -# ---------------------------------------- +# --------------------------------------------- +# Sparql queries: Table exports / Query Reports +# --------------------------------------------- SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$(V).sparql $(REPORTDIR)/$(V).tsv) # This combines all into one single command -.PHONY: all_reports_onestep -all_reports_onestep: $(SRC) | $(REPORTDIR) +.PHONY: custom_reports +custom_reports: $(SRC) | $(REPORTDIR) ifneq ($(SPARQL_EXPORTS_ARGS),) $(ROBOT) query -f tsv -i $< $(SPARQL_EXPORTS_ARGS) endif @@ -450,7 +446,7 @@ $(ONT)-base.owl: $(SRC) $(OTHER_SRC) --annotation oboInOwl:date "$(OBODATE)" --output $@.tmp.owl && mv $@.tmp.owl $@ # Full: The full artefacts with imports merged, reasoned -$(ONT)-full.owl: $(SRC) $(OTHER_SRC) +$(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES) $(ROBOT) merge --input $< \ reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \ relax \ @@ -458,14 +454,14 @@ $(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --annotation oboInOwl:date "$(OBODATE)" --output $@.tmp.owl && mv $@.tmp.owl $@ # foo-non-classified: (edit->imports-merged) -$(ONT)-non-classified.owl: $(SRC) $(OTHER_SRC) +$(ONT)-non-classified.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES) $(ROBOT) merge --input $< \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --annotation oboInOwl:date "$(OBODATE)" --output $@.tmp.owl && mv $@.tmp.owl $@ # foo-simple: (edit->reason,relax,reduce,drop imports, drop every axiom which contains an entity outside the "namespaces of interest") # drop every axiom: filter --term-file keep_terms.txt --trim true # remove --select imports --trim false \ -$(ONT)-simple.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED) +$(ONT)-simple.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES) $(ROBOT) merge --input $< $(patsubst %, -i %, $(OTHER_SRC)) \ reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \ relax \ @@ -484,12 +480,30 @@ explain_unsat: $(SRC) +# ---------------------------------------- +# General Validation +# ---------------------------------------- +TSV= +ALL_TSV_FILES= + +validate-tsv: $(TSV) | $(TMPDIR) + for FILE in $< ; do \ + tsvalid $$FILE > $(TMPDIR)/validate.txt; \ + if [ -s $(TMPDIR)/validate.txt ]; then cat $(TMPDIR)/validate.txt && exit 1; fi ; \ + done + +validate-all-tsv: $(ALL_TSV_FILES) + make validate-tsv TSV="$^" + +# ---------------------------------------- +# Editors Utilities +# ---------------------------------------- + .PHONY: normalize_src normalize_src: $(SRC) - $(ROBOT) convert -i $< -f ofn -o tmp/normalise && mv tmp/normalise $< - + $(ROBOT) convert -i $< -f ofn -o $(TMPDIR)/normalise && mv $(TMPDIR)/normalise $< .PHONY: validate_idranges validate_idranges: @@ -501,4 +515,71 @@ update_repo: +# Note to future generations: prepending ./ is a safety measure to ensure that +# the environment does not malicously set `CLEANFILES` to `\`. +.PHONY: clean +clean: + [ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/* + [ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/* + rm -f $(CLEANFILES) + +.PHONY: help +help: + @echo "$$data" + +define data +Usage: [IMAGE=(odklite|odkfull)] [ODK_DEBUG=yes] sh run.sh make [(IMP|MIR|IMP_LARGE|PAT)=(false|true)] command + +---------------------------------------- + Command reference +---------------------------------------- + +Core commands: +* prepare_release: Run the entire release pipeline. Use make IMP=false prepare_release to avoid rerunning the imports +* update_repo: Update the ODK repository setup using the config file vfbext-odk.yaml +* test: Running all validation tests +* odkversion: Show the current version of the ODK Makefile and ROBOT. +* clean: Delete all temporary files +* help: Print ODK Usage information + + +Imports management: +* refresh-imports: Refresh all imports and mirrors. +* no-mirror-refresh-imports: Refresh all imports without downloading mirrors. +* refresh-imports-excluding-large: Refresh all imports and mirrors, but skipping the ones labelled as 'is_large'. +* refresh-%: Refresh a single import, i.e. refresh-go will refresh 'imports/go_import.owl'. +* no-mirror-refresh-%: Refresh a single import without updating the mirror, i.e. refresh-go will refresh 'imports/go_import.owl'. +* mirror-%: Refresh a single mirror. + +Editor utilities: +* validate_idranges: Make sure your ID ranges file is formatted correctly +* normalize_src: Load and safe your vfbext-edit file after you to make sure its serialised correctly +* explain_unsat: If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes +* validate-all-tsv: Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files +* validate-tsv: Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv. + +Additional build commands (advanced users) +* all: Run the entire pipeline (like prepare_release), but without copying the release files to the release directory. +* all_subsets: Build all subsets +* custom_reports: Generate all custom sparql reports you have configured in your vfbext-odk.yaml file. +* all_assets: Build all assets +* show_assets: Print a list of all assets that would be build by the release pipeline + +Additional QC commands (advanced users) +* robot_reports: Run all configured ROBOT reports +* validate_profile_%: Run an OWL2 DL profile validation check, for example validate_profile_vfbext-edit.owl. + +Examples: +* sh run.sh make IMP=false prepare_release +* sh run.sh make update_repo +* sh run.sh make test + +Tricks: +* Add -B to the end of your command to force re-running it even if nothing has changed +* Use the IMAGE parameter to the run.sh script to use a different image like odklite +* Use ODK_DEBUG=yes sh run.sh make ... to print information about timing and debugging + +endef +export data + include vfbext.Makefile \ No newline at end of file diff --git a/src/ontology/imports/caro_import.owl b/src/ontology/imports/caro_import.owl index 77ff448..ec05a7b 100644 --- a/src/ontology/imports/caro_import.owl +++ b/src/ontology/imports/caro_import.owl @@ -7,17 +7,19 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:caro="http://purl.obolibrary.org/obo/caro#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> - - - 2022-01-24 + + None + + Common Anatomy Reference Ontology + + Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendal. + 2022-02-18 + 2022-02-25 @@ -45,21 +47,18 @@ - - - - - - - - - - - - - + + IAO:0000112 + uberon + example_of_usage + true + example_of_usage + + example of usage + example of usage + @@ -75,43 +74,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + editor note + - + + + elucidation + @@ -133,52 +114,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -187,27 +122,15 @@ - - database_cross_reference - - - - - - - - - - - - - + - + + has_obo_namespace + @@ -225,290 +148,39 @@ - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - - has part - - - - - - - - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple - 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 - - 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 - - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - has characteristic - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - 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. - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - 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. - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - 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. - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - + - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - + - + - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - + - - - - - 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. - disposition of - - - + - - - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - overlaps - + - + - - - - For use in recording has_part with a cardinality constraint. - Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ? - has component - + - + - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - + - + - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - + @@ -526,6 +198,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + entity Entity Julius Caesar @@ -575,6 +248,24 @@ A continuant cannot have an occurrent as part: use 'participates in'. 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 + + @@ -611,24 +302,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. (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 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 - - @@ -636,8 +309,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - ic IndependentContinuant a chair @@ -699,393 +370,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - 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. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - 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. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - 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. @@ -1100,69 +388,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - An anatomical entity that has mass. CARO:0000006 @@ -1171,362 +400,15 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - - - - - - - - - - - - - Anatomical entity that has no mass. - CARO:0000007 - - immaterial anatomical entity - - - - - - - - - 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 - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 - - - - - - - - - - - - - - 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 - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - 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 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. - mah - 10.7.2011 - - gross anatomical part - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - An individual member of a clade of cellular organisms. - mah - 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 - - - - - - - - - - - - - - - - - - 2 - - - - - - Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. - CARO:0000054 - - disconnected anatomical group - - - - - - - - - - - - - - - An anatomical structure consisting of one or more cells. 2018-09-28T14:20:19Z cellular anatomical structure dos - - - - - - - - - - - - - - - With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell - @@ -1545,460 +427,9 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. expression pattern - - - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - - - - - - Viruses - - - - - - - - - Viroids - - - - - - - - - cellular organisms - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. - trait - quality - PATO:0000001 - quality - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. - PATOC:GVG - - - - - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - quality - PATO:0000051 - morphology - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - PATOC:GVG - - - - - - - - - shape - - - - - - - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - PATO:0000125 - mass - - - - - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - relational structural quality - quality - PATO:0000141 - structure - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATOC:GVG - - - - - - - - - physical quality - - - - - - - - - A quality which inheres in a continuant. - monadic quality of a continuant - multiply inhering quality of a physical entity - quality of a continuant - quality of a single physical entity - quality of an object - quality of continuant - monadic quality of an object - monadic quality of continuant - quality - PATO:0001241 - physical object quality - - - - - A quality which inheres in a continuant. - PATOC:GVG - - - - - - - - - cellularity - - - - - - - - - multicellular - - - - - - - - - organismal quality - - - - - - - - - 3-D shape - - - - - - - - - maximally connected - - - - - - - - - disconnected - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Should belong in BFO, but lives in caro for now. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/imports/fbbt_import.owl b/src/ontology/imports/fbbt_import.owl index 99d2125..b67178f 100644 --- a/src/ontology/imports/fbbt_import.owl +++ b/src/ontology/imports/fbbt_import.owl @@ -18,9 +18,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2022-01-24 + + + 2022-02-25 @@ -301,24 +301,12 @@ - - - - - - - - - - - - @@ -331,12 +319,6 @@ - - - - - - @@ -2536,7 +2518,7 @@ For example, A and B may be gene products and binding of B by A positively regul 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 + CARO:MAH FBC:DOS @@ -2615,7 +2597,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity which is part_of Drosophila melanogaster. - CARO:MAH + CARO:MAH diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index 0a20319..e650d8d 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -8,8 +8,8 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - - 2022-01-24 + + 2022-02-25 diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index abf2eca..9f9d2eb 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -16,9 +16,9 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2022-01-24 + + + 2022-02-25 diff --git a/src/ontology/reports/validate_profile_owl2dl_vfbext.owl.txt b/src/ontology/reports/validate_profile_owl2dl_vfbext.owl.txt new file mode 100644 index 0000000..9625e2e --- /dev/null +++ b/src/ontology/reports/validate_profile_owl2dl_vfbext.owl.txt @@ -0,0 +1 @@ +OWL 2 DL Profile Report: [Ontology and imports closure in profile] diff --git a/src/ontology/vfbext-edit.owl b/src/ontology/vfbext-edit.owl index bd9f56a..e1e65c9 100644 --- a/src/ontology/vfbext-edit.owl +++ b/src/ontology/vfbext-edit.owl @@ -18,7 +18,7 @@ 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/3.0/") +Annotation(terms:license "https://creativecommons.org/licenses/by/4.0/") Annotation(rdfs:comment "VFB extension ontology") Declaration(Class(vfb:VFB_10000005)) diff --git a/src/ontology/vfbext-odk.yaml b/src/ontology/vfbext-odk.yaml index 4e94eb4..78f30b5 100644 --- a/src/ontology/vfbext-odk.yaml +++ b/src/ontology/vfbext-odk.yaml @@ -21,6 +21,7 @@ import_group: products: - id: ro - id: caro + module_type: custom - id: fbbt - id: obi module_type: minimal diff --git a/src/ontology/vfbext.Makefile b/src/ontology/vfbext.Makefile index 69f4c4e..d2b0c61 100644 --- a/src/ontology/vfbext.Makefile +++ b/src/ontology/vfbext.Makefile @@ -7,13 +7,20 @@ # Add VFB iri $(ONT).owl: $(ONT)-full.owl grep -v owl:versionIRI $< > $@.tmp.owl - $(ROBOT) annotate -i $@.tmp.owl --ontology-iri http://virtualflybrain.org/data/VFB/OWL/vfbext.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 + # Include copying import files .PHONY: prepare_release -prepare_release: $(ASSETS) $(PATTERN_RELEASE_FILES) +prepare_release: $(ASSETS) rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ rsync -R $(IMPORT_FILES) $(RELEASEDIR) &&\ rm -f $(CLEANFILES) &&\ diff --git a/src/sparql/def-lacks-xref-violation.sparql b/src/sparql/def-lacks-xref-violation.sparql deleted file mode 100644 index cff9773..0000000 --- a/src/sparql/def-lacks-xref-violation.sparql +++ /dev/null @@ -1,12 +0,0 @@ -prefix oio: -prefix def: -prefix owl: - -SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE -{ - ?cls a owl:Class . - OPTIONAL { ?cls oio:hasDbXref ?xref } . - OPTIONAL { ?cls def: ?def } . - FILTER (!isBlank(?cls)) -} -GROUP BY ?cls ?def diff --git a/src/sparql/equivalent-classes-violation.sparql b/src/sparql/equivalent-classes-violation.sparql deleted file mode 100644 index ed5ccdd..0000000 --- a/src/sparql/equivalent-classes-violation.sparql +++ /dev/null @@ -1,14 +0,0 @@ -prefix oio: -prefix owl: -prefix rdfs: - -SELECT ?baseClass ?baseLabel ?equivalentClass ?equivalentLabel WHERE -{ - ?baseClass owl:equivalentClass ?equivalentClass . - ?baseClass rdfs:label ?baseLabel . - ?equivalentClass rdfs:label ?equivalentLabel . - - FILTER (!isBlank(?baseClass)) . - FILTER (!isBlank(?equivalentClass)) - -} diff --git a/src/sparql/iri-range-violation.sparql b/src/sparql/iri-range-violation.sparql new file mode 100644 index 0000000..ff4fb9e --- /dev/null +++ b/src/sparql/iri-range-violation.sparql @@ -0,0 +1,19 @@ +PREFIX never_in_taxon: +PREFIX present_in_taxon: +PREFIX oboInOwl: +PREFIX dcterms: +PREFIX foaf: + +SELECT ?term ?property ?value +WHERE { + VALUES ?property { + never_in_taxon: + present_in_taxon: + foaf:depicted_by + oboInOwl:inSubset + dcterms:contributor } + ?term ?property ?value . + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/VFBEXT_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_"))) + FILTER (!isIRI(?value)) +} + diff --git a/src/sparql/label-with-iri-violation.sparql b/src/sparql/label-with-iri-violation.sparql new file mode 100644 index 0000000..8466ebd --- /dev/null +++ b/src/sparql/label-with-iri-violation.sparql @@ -0,0 +1,9 @@ +PREFIX rdfs: + +SELECT ?term ?value +WHERE { + ?term rdfs:label ?value . + FILTER (REGEX(?value, "http[s]?[:]")) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/VFBEXT_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_"))) +} + diff --git a/src/sparql/nolabels-violation.sparql b/src/sparql/nolabels-violation.sparql deleted file mode 100644 index d506a41..0000000 --- a/src/sparql/nolabels-violation.sparql +++ /dev/null @@ -1,13 +0,0 @@ -PREFIX owl: -PREFIX rdf: -PREFIX rdfs: -PREFIX replaced_by: - -SELECT ?cls WHERE { - ?cls a owl:Class - FILTER NOT EXISTS {?cls rdfs:label ?lab} - FILTER NOT EXISTS {?cls replaced_by: ?replCls} - FILTER (!isBlank(?cls)) - FILTER ( regex(str(?cls), "^http://purl.obolibrary.org/obo/GO_")) -} -ORDER BY ?cls diff --git a/src/sparql/obsolete-violation.sparql b/src/sparql/obsolete-violation.sparql deleted file mode 100644 index c81bf71..0000000 --- a/src/sparql/obsolete-violation.sparql +++ /dev/null @@ -1,24 +0,0 @@ -prefix xsd: -PREFIX owl: -PREFIX rdf: -PREFIX rdfs: -PREFIX replaced_by: -PREFIX consider: - -SELECT ?cls ?clsLabel ?rule WHERE { - ?cls a owl:Class ; - rdfs:label ?clsLabel ; - owl:deprecated "true"^^xsd:boolean - { - { - FILTER ( ! regex(str(?clsLabel), "^obsolete ") ) - BIND ("obsolete label must start with obsolete" AS ?rule) - } - UNION - { - ?cls rdfs:subClassOf ?parent - BIND("no logical axioms for obsolete" AS ?rule) - } - } -} -ORDER BY ?cls diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql index 63857fe..0784a1d 100644 --- a/src/sparql/owldef-self-reference-violation.sparql +++ b/src/sparql/owldef-self-reference-violation.sparql @@ -1,11 +1,12 @@ -prefix rdf: -prefix oio: -prefix owl: -prefix rdfs: +PREFIX rdf: +PREFIX oio: +PREFIX owl: +PREFIX rdfs: -SELECT ?c -WHERE { - { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?c ] ] } +SELECT ?term WHERE { + { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] } UNION - { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?c ] ] ] } + { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] } + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/VFBEXT_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_"))) } + diff --git a/src/sparql/owldef-violation.sparql b/src/sparql/owldef-violation.sparql deleted file mode 100644 index 3b59f88..0000000 --- a/src/sparql/owldef-violation.sparql +++ /dev/null @@ -1,9 +0,0 @@ -prefix oio: -prefix owl: -prefix rdfs: - -WELECT * -WHERE { - ?c rdfs:subClassOf ?d ; - owl:equivalentClass [ - owl:intersectionOf TODO diff --git a/src/sparql/redundant-subClassOf-violation.sparql b/src/sparql/redundant-subClassOf-violation.sparql deleted file mode 100644 index bed15cd..0000000 --- a/src/sparql/redundant-subClassOf-violation.sparql +++ /dev/null @@ -1,15 +0,0 @@ -prefix oio: -prefix owl: -prefix rdfs: - -SELECT ?x ?xl ?y ?yl ?z ?zl WHERE -{ - ?x rdfs:subClassOf ?y ; - rdfs:label ?xl . - ?y rdfs:subClassOf+ ?z ; - rdfs:label ?yl . - ?x rdfs:subClassOf ?z . - ?z rdfs:label ?zl . - - -} diff --git a/src/sparql/trailing-whitespace-violation.sparql b/src/sparql/trailing-whitespace-violation.sparql deleted file mode 100644 index 1d69472..0000000 --- a/src/sparql/trailing-whitespace-violation.sparql +++ /dev/null @@ -1,11 +0,0 @@ -# home: hp/sparql/trailing-whitespace-violation.sparql -prefix owl: -prefix rdfs: - -SELECT ?c ?p ?x WHERE -{ - ?c ?p ?x . - - FILTER( regex(STR(?x), "^ ") || regex(STR(?x), " $") ) - FILTER( ?p != owl:annotatedTarget ) -} diff --git a/src/sparql/vfbext_terms.sparql b/src/sparql/vfbext_terms.sparql index 4e1173b..305fff9 100644 --- a/src/sparql/vfbext_terms.sparql +++ b/src/sparql/vfbext_terms.sparql @@ -3,5 +3,5 @@ WHERE { { ?s1 ?p1 ?term . } UNION { ?term ?p2 ?o2 . } - FILTER(isIRI(?term) && (regex(str(?term), UCASE("vfbext_")) || regex(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_") || regex(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/VFBEXT_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/fbbt/vfb/VFB_"))) } diff --git a/src/sparql/xref-syntax-violation.sparql b/src/sparql/xref-syntax-violation.sparql deleted file mode 100644 index 98a6172..0000000 --- a/src/sparql/xref-syntax-violation.sparql +++ /dev/null @@ -1,13 +0,0 @@ -# home: hp -prefix hasDbXref: -prefix oio: -prefix owl: -prefix rdfs: - -SELECT ?c ?x WHERE -{ - ?c hasDbXref: ?x . - - FILTER( regex(STR(?x), " ") || regex(STR(?x), ";") || STR(?x) = "" ) - -} diff --git a/vfbext-base.json b/vfbext-base.json index 90255da..a6242fe 100644 --- a/vfbext-base.json +++ b/vfbext-base.json @@ -94,11 +94,11 @@ }, { "pred": "http://purl.org/dc/terms/license", - "val": "https://creativecommons.org/licenses/by/3.0/" + "val": "https://creativecommons.org/licenses/by/4.0/" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:01:2022 13:13" + "val": "25:02:2022 15:21" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -106,11 +106,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-01-24" + "val": "2022-02-25" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-01-24/vfbext-base.json", + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/vfbext-base.json", "xrefs": [] }, "nodes": [ diff --git a/vfbext-base.obo b/vfbext-base.obo index 6a2f681..f23bbfb 100644 --- a/vfbext-base.obo +++ b/vfbext-base.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2022-01-24/vfbext-base.owl -date: 24:01:2022 13:13 +data-version: vfbext/releases/2022-02-25/vfbext-base.owl +date: 25:02:2022 15:21 subsetdef: clone "" subsetdef: neuron "" subsetdef: ns_part "" @@ -11,8 +11,8 @@ ontology: vfbext/vfbext-base 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/elements/1.1/type IAO:8000001 -property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/ xsd:string -property_value: owl:versionInfo "2022-01-24" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string +property_value: owl:versionInfo "2022-02-25" xsd:string [Term] id: VFB:10000005 diff --git a/vfbext-base.owl b/vfbext-base.owl index 2f6dd14..5cd863a 100644 --- a/vfbext-base.owl +++ b/vfbext-base.owl @@ -13,14 +13,14 @@ xmlns:terms="http://purl.org/dc/terms/" 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/3.0/</terms:license> - 24:01:2022 13:13 + https://creativecommons.org/licenses/by/4.0/</terms:license> + 25:02:2022 15:21 VFB extension ontology - 2022-01-24 + 2022-02-25 diff --git a/vfbext-full.json b/vfbext-full.json index 03cdc6d..27be4a6 100644 --- a/vfbext-full.json +++ b/vfbext-full.json @@ -335,11 +335,6 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/BFO_0000040" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000004", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/BFO_0000141" - }, { "obj": "http://purl.obolibrary.org/obo/BFO_0000004", "pred": "is_a", @@ -395,11 +390,6 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/CARO_0000006" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000040", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0001010" - }, { "obj": "http://purl.obolibrary.org/obo/BFO_0000050", "pred": "subPropertyOf", @@ -445,141 +435,21 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002411" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000141", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000007" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000000", "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/CARO_0000006" }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000000", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000007" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000000", "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/FBbt_10000000" }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "http://purl.obolibrary.org/obo/RO_0002180", - "sub": "http://purl.obolibrary.org/obo/CARO_0020000" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000014" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000040" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000042" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0010000" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000006", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000003" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000006", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0001008" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000006", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0020000" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000006", "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/CARO_0020003" }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000012", - "pred": "http://purl.obolibrary.org/obo/BFO_0000050", - "sub": "http://purl.obolibrary.org/obo/CARO_0001008" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000013", - "pred": "http://purl.obolibrary.org/obo/BFO_0000050", - "sub": "http://purl.obolibrary.org/obo/CARO_0000014" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000013", - "pred": "http://purl.obolibrary.org/obo/BFO_0000051", - "sub": "http://purl.obolibrary.org/obo/CARO_0030002" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000013", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CL_0000003" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000004" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000040" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000042" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0001000" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0010000" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001010", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/NCBITaxon_10239" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001010", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/NCBITaxon_12884" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0010000", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000032" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0010004", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000012" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0010004", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/NCBITaxon_131567" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0020003", "pred": "is_a", @@ -595,11 +465,6 @@ "pred": "http://purl.obolibrary.org/obo/BFO_0000050", "sub": "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004" }, - { - "obj": "http://purl.obolibrary.org/obo/CL_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000013" - }, { "obj": "http://purl.obolibrary.org/obo/FBbt_00007001", "pred": "is_a", @@ -645,106 +510,11 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/GO_0016301" }, - { - "obj": "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000012" - }, - { - "obj": "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0010004" - }, { "obj": "http://purl.obolibrary.org/obo/NCBITaxon_7227", "pred": "http://purl.obolibrary.org/obo/BFO_0000050", "sub": "http://purl.obolibrary.org/obo/FBbt_10000000" }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000001", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001241" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000051", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000052" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000051", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000141" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000052", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0002266" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000125", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0000006" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000141", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0010000" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000141", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0010001" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001018", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000125" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001241", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000051" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001241", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001018" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001241", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001995" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001992", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001993" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001993", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0010000" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001995", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001992" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0002266", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0000003" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0010000", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0000003" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0010001", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0020000" - }, { "obj": "http://purl.obolibrary.org/obo/RO_0000052", "pred": "subPropertyOf", @@ -1461,9 +1231,9 @@ "sub": "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007" }, { - "obj": "http://www.w3.org/2002/07/owl#topObjectProperty", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002131" + "obj": "http://www.w3.org/2002/07/owl#Thing", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/BFO_0000001" }, { "obj": "http://xmlns.com/foaf/0.1/image", @@ -1476,62 +1246,9 @@ "sub": "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014" } ], - "equivalentNodesSets": [ - { - "nodeIds": [ - "http://purl.obolibrary.org/obo/CARO_0000013", - "http://purl.obolibrary.org/obo/CL_0000003" - ] - }, - { - "nodeIds": [ - "http://purl.obolibrary.org/obo/CARO_0010004", - "http://purl.obolibrary.org/obo/NCBITaxon_131567" - ] - } - ], + "equivalentNodesSets": [], "id": "http://purl.obolibrary.org/obo/vfbext/vfbext-full.json", "logicalDefinitionAxioms": [ - { - "definedClassId": "http://purl.obolibrary.org/obo/CARO_0000003", - "genusIds": [ - "http://purl.obolibrary.org/obo/CARO_0000006" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0002266", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - }, - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0010000", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - } - ] - }, - { - "definedClassId": "http://purl.obolibrary.org/obo/CARO_0000006", - "genusIds": [ - "http://purl.obolibrary.org/obo/CARO_0000000" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0000125", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - } - ] - }, - { - "definedClassId": "http://purl.obolibrary.org/obo/CARO_0010000", - "genusIds": [ - "http://purl.obolibrary.org/obo/CARO_0000003" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0001993", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - } - ] - }, { "definedClassId": "http://purl.obolibrary.org/obo/FBbt_10000000", "genusIds": [ @@ -1569,11 +1286,11 @@ }, { "pred": "http://purl.org/dc/terms/license", - "val": "https://creativecommons.org/licenses/by/3.0/" + "val": "https://creativecommons.org/licenses/by/4.0/" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:01:2022 13:12" + "val": "25:02:2022 15:21" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -1581,11 +1298,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-01-24" + "val": "2022-02-25" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-01-24/vfbext-full.json", + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/vfbext-full.json", "xrefs": [] }, "nodes": [ @@ -1811,1132 +1528,339 @@ "type": "CLASS" }, { - "id": "http://purl.obolibrary.org/obo/BFO_0000016", - "lbl": "disposition", + "id": "http://purl.obolibrary.org/obo/BFO_0000017", + "lbl": "realizable entity", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000020", + "lbl": "specifically dependent continuant", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000023", + "lbl": "role", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000031", + "lbl": "generically dependent continuant", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000040", + "lbl": "material entity", + "meta": { + "definition": { + "val": "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl": "part_of", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "disposition" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "is part of" }, { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Disposition" + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "my brain is part of my body (continuant parthood, two material entities)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an atom of element X has the disposition to decay to an atom of element Y" + "val": "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "certain people have a predisposition to colon cancer" + "val": "this day is part of this year (occurrent parthood)" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "children are innately disposed to categorize objects in certain ways." + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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/" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." + "val": "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'." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "part_of" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" + "pred": "http://purl.obolibrary.org/obo/RO_0001900", + "val": "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000017", - "lbl": "realizable entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "realizable" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "RealizableEntity" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the disposition of this piece of metal to conduct electricity." + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000017" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the disposition of your blood to coagulate" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000019" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of your reproductive organs" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000020" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of being a doctor" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000031" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of this boundary to delineate where Utah and Colorado meet" + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "external" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "relationship" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "part_of" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://www.obofoundry.org/ro/#OBO_REL:part_of" } ], "definition": { - "val": "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.", + "val": "a core relation that holds between a part and its whole", "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000019", - "lbl": "quality", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "quality" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Quality" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the ambient temperature of this portion of air" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the color of a tomato" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the length of the circumference of your waist" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the mass of this piece of gold." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the shape of your nose" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the shape of your nostril" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " - }, + }, + "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": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " + "val": "BFO:0000050" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "val": "OBO_REL:part_of" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/BFO_0000020", - "lbl": "specifically dependent continuant", + "id": "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl": "has_part", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "sdc" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "SpecificallyDependentContinuant" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "of one-sided specifically dependent continuants: the mass of this tomato" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the disposition of this fish to decay" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has part" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of this heart: to pump blood" + "val": "my body has part my brain (continuant parthood, two material entities)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the mutual dependence of proton donors and acceptors in chemical reactions [79" + "val": "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" + "val": "this year has part this day (occurrent parthood)" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the pink color of a medium rare piece of grilled filet mignon at its center" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of being a doctor" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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/" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the shape of this hole." + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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'." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the smell of this portion of mozzarella" + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "has_part" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." + "pred": "http://purl.obolibrary.org/obo/RO_0001900", + "val": "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "external" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "relationship" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "has_part" } ], "definition": { - "val": "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])", + "val": "a core relation that holds between a whole and its part", "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000023", - "lbl": "role", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "role" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Role" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the priest role" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of a boundary to demarcate two neighboring administrative territories" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of a building in serving as a military target" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of a stone in marking a property boundary" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of subject in a clinical trial" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the student role" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" - }, + }, + "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": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " + "val": "BFO:0000051" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "val": "OBO_REL:has_part" } - ], - "definition": { - "val": "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.", - "xrefs": [] - } + ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/BFO_0000031", - "lbl": "generically dependent continuant", + "id": "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl": "preceded by", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "gdc" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "GenericallyDependentContinuant" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "preceded by" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000034", - "lbl": "function", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "function" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Function" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of a hammer to drive in nails" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of a heart pacemaker to regulate the beating of a heart through electricity" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of amylase in saliva to break down starch into sugar" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000040", - "lbl": "material entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "material" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "MaterialEntity" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a flame" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a forest fire" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a human being" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a hurricane" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a photon" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a puff of smoke" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a sea wave" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a tornado" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an aggregate of human beings." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an energy wave" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an epidemic" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the undetached arm of a human being" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "definition": { - "val": "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl": "part_of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "is part of" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my brain is part of my body (continuant parthood, two material entities)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this day is part of this year (occurrent parthood)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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/" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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'." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "part_of" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/BFO" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000002" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000003" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000004" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000017" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000019" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000020" - }, - { - "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": "external" - }, - { - "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" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://www.obofoundry.org/ro/#OBO_REL:part_of" - } - ], - "definition": { - "val": "a core relation that holds between a part and its whole", - "xrefs": [] - }, - "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" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl": "has_part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "has part" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my body has part my brain (continuant parthood, two material entities)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this year has part this day (occurrent parthood)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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/" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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'." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "has_part" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/BFO" - }, - { - "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": "external" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "has_part" - } - ], - "definition": { - "val": "a core relation that holds between a whole and its part", - "xrefs": [] - }, - "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" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl": "preceded by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "is preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "preceded_by" - }, - { - "pred": "http://purl.org/dc/elements/1.1/source", - "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl": "precedes", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "precedes" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000141", - "lbl": "immaterial entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "immaterial" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "ImmaterialEntity" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000000", - "lbl": "anatomical entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/caro.owl" - } - ], - "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." - ], - "definition": { - "val": "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.", - "xrefs": [ - "CAROC:Brownsville2014" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000003", - "lbl": "connected anatomical structure", - "meta": { - "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." - ], - "definition": { - "val": "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000004", - "lbl": "organism substance", - "meta": { - "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." - } - ], - "comments": [ - "Note - CARO explicitly declares organisms substances to be part of (some) organism." - ], - "definition": { - "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.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "portion of organism substance", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000006", - "lbl": "material anatomical entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/caro.owl" - } - ], - "definition": { - "val": "An anatomical entity that has mass.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000007", - "lbl": "immaterial anatomical entity", - "meta": { - "definition": { - "val": "Anatomical entity that has no mass.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000012", - "lbl": "multicellular organism", - "meta": { - "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." - ], - "definition": { - "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000013", - "lbl": "cell", - "meta": { - "comments": [ - "deprecate and replace with CL or GO term?" - ], - "definition": { - "val": "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", - "xrefs": [] - }, - "xrefs": [ - { - "val": "CL:0000000" - }, - { - "val": "GO:0005623" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000014", - "lbl": "cell part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "cell component" - } - ], - "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." - ], - "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000032", - "lbl": "organism subdivision", - "meta": { - "basicPropertyValues": [ - { - "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." - } - ], - "definition": { - "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": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000040", - "lbl": "acellular anatomical structure", - "meta": { - "comments": [ - "Example. Insect cuticle, eggshell, hair." - ], - "definition": { - "val": "An anatomical structure that has no cells or cell parts as a part.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000042", - "lbl": "extraembryonic structure", - "meta": { - "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" - ], - "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#plus" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0001000", - "lbl": "multi-cell-part structure", - "meta": { - "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "multi-cell-component structure" - } - ], - "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." - ], - "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0001008", - "lbl": "gross anatomical part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "mah" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "10.7.2011" - } - ], - "definition": { - "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. ", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#plus" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0001010", - "lbl": "organism or virus or viroid", - "meta": { - "basicPropertyValues": [ + "val": "is preceded by" + }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Melissa Haendel" + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "preceded_by" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "9/18/11" + "pred": "http://purl.org/dc/elements/1.1/source", + "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ], "definition": { - "val": "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.", + "val": "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.", "xrefs": [] - } + }, + "subsets": [ + "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" + ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/CARO_0010000", - "lbl": "multicellular anatomical structure", + "id": "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl": "precedes", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "djs93" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "Sun Feb 27 10:53:00 GMT 2011" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "precedes" } ], "definition": { - "val": "An anatomical structure that has more than one cell as a part.", + "val": "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.", "xrefs": [] }, "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" + "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/CARO_0010004", - "lbl": "cellular organism", + "id": "http://purl.obolibrary.org/obo/CARO_0000000", + "lbl": "anatomical entity", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "mah" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "7.16.2011" + "pred": "http://purl.obolibrary.org/obo/IAO_0000412", + "val": "http://purl.obolibrary.org/obo/caro.owl" } ], "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. " + "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." ], "definition": { - "val": "An individual member of a clade of cellular organisms.", - "xrefs": [] + "val": "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.", + "xrefs": [ + "CAROC:Brownsville2014" + ] } }, "type": "CLASS" }, { - "id": "http://purl.obolibrary.org/obo/CARO_0020000", - "lbl": "disconnected anatomical group", + "id": "http://purl.obolibrary.org/obo/CARO_0000006", + "lbl": "material anatomical entity", "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000412", + "val": "http://purl.obolibrary.org/obo/caro.owl" + } + ], "definition": { - "val": "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", + "val": "An anatomical entity that has mass.", "xrefs": [] }, "subsets": [ @@ -2991,26 +1915,6 @@ }, "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/CL_0000003", - "lbl": "native cell", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/cl.owl" - } - ], - "comments": [ - "To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12)." - ], - "definition": { - "val": "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).", - "xrefs": [] - } - }, - "type": "CLASS" - }, { "id": "http://purl.obolibrary.org/obo/FBbt_00007001", "lbl": "anatomical structure", @@ -3233,60 +2137,94 @@ "type": "CLASS" }, { - "id": "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl": "definition", + "id": "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl": "example of usage", "meta": { "basicPropertyValues": [ { - "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": "uberon" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val": "true" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "example_of_usage" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } + ], + "xrefs": [ + { + "val": "IAO:0000112" + } ] }, "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_10239", - "lbl": "Viruses", + "id": "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl": "definition", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val": "http://purl.obolibrary.org/obo/iao.owl" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_12884", - "lbl": "Viroids", + "id": "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl": "editor note", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" + "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#shorthand", + "val": "editor_note" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val": "http://purl.obolibrary.org/obo/iao.owl" + } + ], + "xrefs": [ + { + "val": "IAO:0000116" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "lbl": "cellular organisms", + "id": "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl": "elucidation", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" + "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val": "http://purl.obolibrary.org/obo/iao.owl" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000293", @@ -3373,33 +2311,7 @@ } ], "definition": { - "val": "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.", - "xrefs": [ - "PATOC:GVG" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "trait", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000051", - "lbl": "morphology", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "quality" - } - ], - "definition": { - "val": "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.", + "val": "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities", "xrefs": [ "PATOC:GVG" ] @@ -3407,104 +2319,6 @@ }, "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000125", - "lbl": "mass", - "meta": { - "definition": { - "val": "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000141", - "lbl": "structure", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "quality" - } - ], - "definition": { - "val": "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.", - "xrefs": [ - "PATOC:GVG" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "relational structural quality", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001241", - "lbl": "physical object quality", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "quality" - } - ], - "definition": { - "val": "A quality which inheres in a continuant.", - "xrefs": [ - "PATOC:GVG" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "monadic quality of a continuant", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "multiply inhering quality of a physical entity ", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of a continuant", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of a single physical entity", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of an object", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of continuant", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "val": "monadic quality of an object", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "val": "monadic quality of continuant", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, { "id": "http://purl.obolibrary.org/obo/RO_0000052", "lbl": "characteristic of", @@ -3556,7 +2370,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0000053", - "lbl": "has_characteristic", + "lbl": "has characteristic", "meta": { "basicPropertyValues": [ { @@ -4245,10 +3059,6 @@ "val": "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ], - "comments": [ - "For use in recording has_part with a cardinality constraint.", - "Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ?" - ], "definition": { "val": "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.", "xrefs": [] @@ -4451,7 +3261,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0002215", - "lbl": "capable of", + "lbl": "capable_of", "meta": { "basicPropertyValues": [ { @@ -6374,6 +5184,21 @@ }, "type": "CLASS" }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000016", + "lbl": "disposition", + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000019", + "lbl": "quality", + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000034", + "lbl": "function", + "type": "CLASS" + }, { "id": "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", "lbl": "has_exemplar", @@ -6399,46 +5224,6 @@ "lbl": "transferase activity, transferring phosphorus-containing groups", "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000052", - "lbl": "shape", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001018", - "lbl": "physical quality", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001992", - "lbl": "cellularity", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001993", - "lbl": "multicellular", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001995", - "lbl": "organismal quality", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0002266", - "lbl": "3-D shape", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0010000", - "lbl": "maximally connected", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0010001", - "lbl": "disconnected", - "type": "CLASS" - }, { "id": "http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0", "lbl": "exemplar_of", @@ -6504,6 +5289,11 @@ "lbl": "database_cross_reference", "type": "PROPERTY" }, + { + "id": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "lbl": "has_obo_namespace", + "type": "PROPERTY" + }, { "id": "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl": "in_subset", diff --git a/vfbext-full.obo b/vfbext-full.obo index 7345884..9b13ea4 100644 --- a/vfbext-full.obo +++ b/vfbext-full.obo @@ -1,8 +1,7 @@ format-version: 1.2 -data-version: vfbext/releases/2022-01-24/vfbext-full.owl -date: 24:01:2022 13:12 +data-version: vfbext/releases/2022-02-25/vfbext-full.owl +date: 25:02:2022 15:21 subsetdef: clone "" -subsetdef: core "" subsetdef: cur "" subsetdef: EmbDevSlim "" subsetdef: goslim_aspergillus "" @@ -20,7 +19,6 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: larval_OF "" subsetdef: neuron "" subsetdef: ns_part "" -subsetdef: plus "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: synaptic_neuropil "" @@ -29,20 +27,20 @@ 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/3.0/ xsd:string -property_value: owl:versionInfo "2022-01-24" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string +property_value: owl:versionInfo "2022-02-25" xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string -property_value: IAO:0000112 "Julius Caesar" xsd:string -property_value: IAO:0000112 "the Second World War" xsd:string -property_value: IAO:0000112 "Verdi’s Requiem" xsd:string -property_value: IAO:0000112 "your body mass index" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: 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 @@ -55,8 +53,8 @@ disjoint_from: BFO:0000003 ! occurrent relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string -property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: 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"} @@ -80,21 +78,20 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string -property_value: IAO:0000112 "a chair" xsd:string -property_value: IAO:0000112 "a heart" xsd:string -property_value: IAO:0000112 "a leg" xsd:string -property_value: IAO:0000112 "a molecule" xsd:string -property_value: IAO:0000112 "a spatial region" xsd:string -property_value: IAO:0000112 "an atom" xsd:string -property_value: IAO:0000112 "an orchestra." xsd:string -property_value: IAO:0000112 "an organism" xsd:string -property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string -property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: 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"} @@ -113,18 +110,6 @@ id: BFO:0000016 name: disposition is_a: BFO:0000017 ! realizable entity disjoint_from: BFO:0000023 ! role -property_value: BFO:0000179 "disposition" xsd:string -property_value: BFO:0000180 "Disposition" xsd:string -property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string -property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string -property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string -property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string -property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 @@ -133,152 +118,44 @@ def: "A specifically dependent continuant that inheres in continuant entities is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality relationship: part_of BFO:0000017 ! realizable entity -property_value: BFO:0000179 "realizable" xsd:string -property_value: BFO:0000180 "RealizableEntity" xsd:string -property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string -property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string -property_value: IAO:0000112 "the function of your reproductive organs" xsd:string -property_value: IAO:0000112 "the role of being a doctor" xsd:string -property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string -property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant relationship: part_of BFO:0000019 ! quality -property_value: BFO:0000179 "quality" xsd:string -property_value: BFO:0000180 "Quality" xsd:string -property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string -property_value: IAO:0000112 "the color of a tomato" xsd:string -property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string -property_value: IAO:0000112 "the mass of this piece of gold." xsd:string -property_value: IAO:0000112 "the shape of your nose" xsd:string -property_value: IAO:0000112 "the shape of your nostril" xsd:string -property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} -def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000020 ! specifically dependent continuant -property_value: BFO:0000179 "sdc" xsd:string -property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string -property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string -property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string -property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string -property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string -property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string -property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string -property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string -property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string -property_value: IAO:0000112 "the role of being a doctor" xsd:string -property_value: IAO:0000112 "the shape of this hole." xsd:string -property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} -property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} -property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role def: "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." [] is_a: BFO:0000017 ! realizable entity -property_value: BFO:0000179 "role" xsd:string -property_value: BFO:0000180 "Role" xsd:string -property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string -property_value: IAO:0000112 "the priest role" xsd:string -property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string -property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string -property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string -property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string -property_value: IAO:0000112 "the student role" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string -property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant def: "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." [] -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant relationship: part_of BFO:0000031 ! generically dependent continuant -property_value: BFO:0000179 "gdc" xsd:string -property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string -property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string -property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string -property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string -property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000034 name: function is_a: BFO:0000016 ! disposition -property_value: BFO:0000179 "function" xsd:string -property_value: BFO:0000180 "Function" xsd:string -property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string -property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string -property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000040 name: material entity def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant -disjoint_from: BFO:0000141 ! immaterial entity -property_value: BFO:0000179 "material" xsd:string -property_value: BFO:0000180 "MaterialEntity" xsd:string -property_value: IAO:0000112 "a flame" xsd:string -property_value: IAO:0000112 "a forest fire" xsd:string -property_value: IAO:0000112 "a human being" xsd:string -property_value: IAO:0000112 "a hurricane" xsd:string -property_value: IAO:0000112 "a photon" xsd:string -property_value: IAO:0000112 "a puff of smoke" xsd:string -property_value: IAO:0000112 "a sea wave" xsd:string -property_value: IAO:0000112 "a tornado" xsd:string -property_value: IAO:0000112 "an aggregate of human beings." xsd:string -property_value: IAO:0000112 "an energy wave" xsd:string -property_value: IAO:0000112 "an epidemic" xsd:string -property_value: IAO:0000112 "the undetached arm of a human being" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string -property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000141 -name: immaterial entity -is_a: BFO:0000004 ! independent continuant -property_value: BFO:0000179 "immaterial" xsd:string -property_value: BFO:0000180 "ImmaterialEntity" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: CARO:0000000 @@ -288,29 +165,6 @@ comment: Following BFO, material anatomical entities may have immaterial parts ( is_a: CARO:0030000 ! biological entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl -[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: has_characteristic PATO:0002266 ! 3-D shape -intersection_of: has_characteristic PATO:0010000 ! maximally connected -disjoint_from: CARO:0000004 ! organism substance -relationship: has_characteristic PATO:0002266 ! 3-D shape -relationship: has_characteristic PATO:0010000 ! maximally connected - -[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 @@ -318,161 +172,8 @@ def: "An anatomical entity that has mass." [] subset: core is_a: BFO:0000040 ! material entity is_a: CARO:0000000 ! anatomical entity -intersection_of: CARO:0000000 ! anatomical entity -intersection_of: has_characteristic PATO:0000125 ! mass -disjoint_from: CARO:0000007 ! immaterial anatomical entity -relationship: has_characteristic PATO:0000125 ! mass property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl -[Term] -id: CARO:0000007 -name: immaterial anatomical entity -def: "Anatomical entity that has no mass." [] -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 -is_a: NCBITaxon:131567 ! cellular organisms - -[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: CL:0000003 ! native cell -equivalent_to: CL:0000003 ! native cell -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: part_of CARO:0000013 ! 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: part_of CARO:0000012 ! multicellular organism -property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.7.2011" xsd:string -property_value: IAO:0000117 "mah" xsd:string - -[Term] -id: CARO:0001010 -name: organism or virus or viroid -def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] -is_a: BFO:0000040 ! material entity -union_of: NCBITaxon:10239 ! Viruses -union_of: NCBITaxon:12884 ! Viroids -union_of: NCBITaxon:131567 ! cellular organisms -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: has_characteristic 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"} ! multicellular -relationship: has_characteristic PATO:0001993 ! multicellular -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: NCBITaxon:131567 ! cellular organisms -equivalent_to: NCBITaxon:131567 ! cellular organisms -property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string -property_value: IAO:0000117 "mah" xsd:string - -[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: has_characteristic PATO:0010001 ! disconnected -intersection_of: RO:0002180 CARO:0000003 {minCardinality="2"} ! has component connected anatomical structure -relationship: has_characteristic PATO:0010001 ! disconnected -relationship: RO:0002180 CARO:0000003 ! has component connected anatomical structure - [Term] id: CARO:0020003 name: cellular anatomical structure @@ -493,15 +194,6 @@ 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: has_part CARO:0000013 ! cell - -[Term] -id: CL:0000003 -name: native cell -def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [] -comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). -is_a: CARO:0000013 ! cell -property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [Term] id: FBbt:00007001 @@ -603,111 +295,15 @@ id: GO:0016772 name: transferase activity, transferring phosphorus-containing groups is_a: GO:0016740 ! transferase activity -[Term] -id: NCBITaxon:10239 -name: Viruses -is_a: CARO:0001010 ! organism or virus or viroid -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - -[Term] -id: NCBITaxon:12884 -name: Viroids -is_a: CARO:0001010 ! organism or virus or viroid -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - -[Term] -id: NCBITaxon:131567 -name: cellular organisms -is_a: CARO:0010004 ! cellular organism -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -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 property_value: IAO:0000589 "quality (PATO)" xsd:string -[Term] -id: PATO:0000051 -name: morphology -namespace: quality -def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [PATOC:GVG] -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0000052 -name: shape -is_a: PATO:0000051 ! morphology - -[Term] -id: PATO:0000125 -name: mass -def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [] -is_a: PATO:0001018 ! physical quality - -[Term] -id: PATO:0000141 -name: structure -namespace: quality -def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] -synonym: "relational structural quality" EXACT [] -is_a: PATO:0000051 ! morphology - -[Term] -id: PATO:0001018 -name: physical quality -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0001241 -name: physical object quality -namespace: quality -def: "A quality which inheres in a continuant." [PATOC:GVG] -synonym: "monadic quality of a continuant" EXACT [] -synonym: "monadic quality of an object" NARROW [] -synonym: "monadic quality of continuant" NARROW [] -synonym: "multiply inhering quality of a physical entity " EXACT [] -synonym: "quality of a continuant" EXACT [] -synonym: "quality of a single physical entity" EXACT [] -synonym: "quality of an object" EXACT [] -synonym: "quality of continuant" EXACT [] -is_a: PATO:0000001 ! quality - -[Term] -id: PATO:0001992 -name: cellularity -is_a: PATO:0001995 ! organismal quality - -[Term] -id: PATO:0001993 -name: multicellular -is_a: PATO:0001992 ! cellularity - -[Term] -id: PATO:0001995 -name: organismal quality -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0002266 -name: 3-D shape -is_a: PATO:0000052 ! shape - -[Term] -id: PATO:0010000 -name: maximally connected -is_a: PATO:0000141 ! structure - -[Term] -id: PATO:0010001 -name: disconnected -is_a: PATO:0000141 ! structure - [Term] id: VFB:10000005 name: cell cluster @@ -754,9 +350,9 @@ 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: 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 @@ -816,10 +412,10 @@ def: "This relation obtains between an objective specification and a planned pro 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 @@ -829,12 +425,12 @@ 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: 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 @@ -845,8 +441,8 @@ 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: 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: 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:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function @@ -858,8 +454,8 @@ 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: 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: 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:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: characteristic_of ! characteristic_of @@ -870,8 +466,8 @@ 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: 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: 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:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string is_a: characteristic_of ! characteristic_of @@ -881,8 +477,8 @@ inverse_of: RO:0000087 ! has role 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: 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: 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:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function @@ -892,8 +488,8 @@ is_a: has_characteristic ! has characteristic id: RO:0000086 name: has quality def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: 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:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality is_a: has_characteristic ! has characteristic @@ -902,8 +498,8 @@ is_a: has_characteristic ! has characteristic 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: 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: 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:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role @@ -1053,11 +649,9 @@ is_a: BFO:0000063 ! precedes 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." [] -comment: For use in recording has_part with a cardinality constraint. -comment: Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ? 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 @@ -1067,7 +661,7 @@ is_a: has_part ! has part 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: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string +property_value: example_of_usage "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: BFO:0000002 ! continuant @@ -1109,7 +703,7 @@ 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: 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: 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: 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 @@ -1120,7 +714,7 @@ 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: 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: 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: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -1149,7 +743,7 @@ 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: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 @@ -1171,7 +765,7 @@ property_value: RO:0001900 RO:0001901 id: RO:0002327 name: enables subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string @@ -1263,7 +857,7 @@ 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: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: example_of_usage "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 @@ -1312,8 +906,8 @@ inverse_of: RO:0002412 ! immediately causally upstream of id: RO:0002410 name: causally related to def: "This relation groups causal relations between material entities and causal relations between processes" [] +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:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -1344,7 +938,7 @@ id: RO:0002418 name: causally upstream of or within def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] synonym: "affects" RELATED [] -property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true @@ -1395,7 +989,7 @@ 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: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -1409,8 +1003,8 @@ 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: 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: 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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI @@ -1433,7 +1027,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: editor_note "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with @@ -1514,7 +1108,7 @@ property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: 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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -1575,7 +1169,7 @@ 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: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: example_of_usage "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: has_part capable_of is_a: RO:0002328 ! functionally related to @@ -1585,7 +1179,7 @@ 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: 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: 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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity @@ -1596,7 +1190,7 @@ 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: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: example_of_usage "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -1613,7 +1207,7 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: example_of_usage "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 positively_regulates is_a: RO:0002596 ! capable of regulating @@ -1736,7 +1330,7 @@ is_a: RO:0002566 ! causally influences id: RO:0017001 name: utilizes def: "X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y." [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string +property_value: example_of_usage "A diagnostic testing device utilizes a specimen." xsd:string property_value: IAO:0000117 "Asiyah Lin" xsd:string property_value: IAO:0000117 "https://orcid.org/0000-0001-9625-1899 Bill Duncan" xsd:string 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 @@ -1810,8 +1404,8 @@ 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: 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: 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 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 @@ -1843,15 +1437,31 @@ 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: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: has_characteristic ! has characteristic +[Typedef] +id: editor_note +name: editor note +namespace: uberon +xref: IAO:0000116 +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + +[Typedef] +id: example_of_usage +name: example of usage +namespace: uberon +xref: IAO:0000112 +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + [Typedef] id: expresses name: expresses @@ -1869,10 +1479,10 @@ 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: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 @@ -1891,15 +1501,14 @@ 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: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: IAO:0000412 http://purl.obolibrary.org/obo/BFO property_value: RO:0001900 RO:0001901 is_transitive: true is_a: overlaps ! overlaps @@ -1965,15 +1574,14 @@ 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: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: IAO:0000412 http://purl.obolibrary.org/obo/BFO property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 @@ -2017,8 +1625,8 @@ 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: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string diff --git a/vfbext-full.owl b/vfbext-full.owl index 3d00e86..d9eae54 100644 --- a/vfbext-full.owl +++ b/vfbext-full.owl @@ -9,7 +9,6 @@ xmlns:vfb="http://purl.obolibrary.org/obo/fbbt/vfb#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:caro="http://purl.obolibrary.org/obo/caro#" xmlns:fbbt="http://purl.obolibrary.org/obo/fbbt#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" @@ -22,13 +21,13 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:oboInOwl2="ttp://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology - https://creativecommons.org/licenses/by/3.0/</terms:license> - 24:01:2022 13:12 + https://creativecommons.org/licenses/by/4.0/</terms:license> + 25:02:2022 15:21 VFB extension ontology - 2022-01-24 + 2022-02-25 @@ -64,7 +63,16 @@ - + + IAO:0000112 + uberon + example_of_usage + true + example_of_usage + + example of usage + example of usage + @@ -87,7 +95,16 @@ - + + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + editor note + @@ -135,7 +152,10 @@ - + + + elucidation + @@ -157,12 +177,6 @@ - - - - - - @@ -251,22 +265,6 @@ - - - - - - - - - - - - - - - - @@ -511,15 +509,11 @@ - - - - - - - + + has_obo_namespace + @@ -543,6 +537,12 @@ + + + + + + @@ -555,6 +555,12 @@ + + + + + + @@ -601,7 +607,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of - @@ -646,7 +651,6 @@ 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 @@ -1238,7 +1242,6 @@ Examples include: the relationship between two channels collected simultaneously - @@ -1247,10 +1250,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - @@ -1295,8 +1294,6 @@ Examples include: the relationship between two channels collected simultaneously 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. - For use in recording has_part with a cardinality constraint. - Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ? has component @@ -2709,6 +2706,7 @@ For example, A and B may be gene products and binding of B by A positively regul + entity Entity Julius Caesar @@ -2937,44 +2935,8 @@ For example, A and B may be gene products and binding of B by A positively regul - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - disposition - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - @@ -2989,45 +2951,9 @@ For example, A and B may be gene products and binding of B by A positively regul - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet 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. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - realizable entity - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - @@ -3041,45 +2967,8 @@ For example, A and B may be gene products and binding of B by A positively regul - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - quality - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - @@ -3094,59 +2983,9 @@ For example, A and B may be gene products and binding of B by A positively regul - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - specifically dependent continuant - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - @@ -3154,34 +2993,9 @@ For example, A and B may be gene products and binding of B by A positively regul - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role 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. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - role - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - @@ -3195,29 +3009,9 @@ For example, A and B may be gene products and binding of B by A positively regul - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - generically dependent continuant - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - @@ -3225,29 +3019,8 @@ For example, A and B may be gene products and binding of B by A positively regul - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - function - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - @@ -3255,83 +3028,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - material entity - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - @@ -3339,10 +3038,6 @@ 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 @@ -3359,89 +3054,11 @@ 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anatomical entity that has mass. CARO:0000006 @@ -3452,387 +3069,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - Anatomical entity that has no mass. - CARO:0000007 - - immaterial anatomical entity - - - - - - - - - - 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 - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 - - - - - - - - - - - - - - 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 - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - 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 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. - mah - 10.7.2011 - - gross anatomical part - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - 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 - - - - - - - - - - An individual member of a clade of cellular organisms. - mah - 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 - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. - CARO:0000054 - - disconnected anatomical group - - - - - - - - - - - - - - - An anatomical structure consisting of one or more cells. 2018-09-28T14:20:19Z cellular anatomical structure dos - - - - - - - - - - - - - - - With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell - @@ -3851,30 +3096,12 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. expression pattern - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - @@ -3892,7 +3119,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process 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 + CARO:MAH FBC:DOS @@ -3971,7 +3198,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process Anatomical entity which is part_of Drosophila melanogaster. - CARO:MAH + CARO:MAH @@ -4065,36 +3292,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - Viruses - - - - - - - - - - Viroids - - - - - - - - - - cellular organisms - - - - @@ -4106,10 +3303,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process 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. quality (PATO) PATO:0000072 - trait quality PATO:0000001 quality @@ -4120,158 +3315,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process 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 quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - quality - PATO:0000051 - morphology - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - PATOC:GVG - - - - - - - - - shape - - - - - - - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - PATO:0000125 - mass - - - - - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - relational structural quality - quality - PATO:0000141 - structure - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATOC:GVG - - - - - - - - - physical quality - - - - - - - - - A quality which inheres in a continuant. - monadic quality of a continuant - multiply inhering quality of a physical entity - quality of a continuant - quality of a single physical entity - quality of an object - quality of continuant - monadic quality of an object - monadic quality of continuant - quality - PATO:0001241 - physical object quality - - - - - A quality which inheres in a continuant. - PATOC:GVG - - - - - - - - - cellularity - - - - - - - - - multicellular - - - - - - - - - organismal quality - - - - - - - - - 3-D shape - - - - - - - - - maximally connected - - - - - - - - - disconnected - @@ -4368,33 +3411,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - Should belong in BFO, but lives in caro for now. - @@ -4428,22 +3444,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - - - - - - diff --git a/vfbext-non-classified.json b/vfbext-non-classified.json index 15a2d5a..36e6680 100644 --- a/vfbext-non-classified.json +++ b/vfbext-non-classified.json @@ -335,11 +335,6 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/BFO_0000040" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000004", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/BFO_0000141" - }, { "obj": "http://purl.obolibrary.org/obo/BFO_0000004", "pred": "is_a", @@ -395,11 +390,6 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/CARO_0000006" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000040", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0001010" - }, { "obj": "http://purl.obolibrary.org/obo/BFO_0000050", "pred": "subPropertyOf", @@ -445,91 +435,21 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002411" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000141", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000007" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000000", "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/CARO_0000006" }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000000", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000007" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000000", "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/FBbt_10000000" }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000013" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000014" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000042" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0010004" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000006", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000004" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000006", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0001008" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000006", "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/CARO_0020003" }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000012", - "pred": "http://purl.obolibrary.org/obo/BFO_0000050", - "sub": "http://purl.obolibrary.org/obo/CARO_0001008" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000013", - "pred": "http://purl.obolibrary.org/obo/BFO_0000050", - "sub": "http://purl.obolibrary.org/obo/CARO_0000014" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000013", - "pred": "http://purl.obolibrary.org/obo/BFO_0000051", - "sub": "http://purl.obolibrary.org/obo/CARO_0030002" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001010", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0010004" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0010000", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000032" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0010004", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000012" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0020003", "pred": "is_a", @@ -585,66 +505,6 @@ "pred": "http://purl.obolibrary.org/obo/BFO_0000050", "sub": "http://purl.obolibrary.org/obo/FBbt_10000000" }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000001", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001241" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000051", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000052" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000051", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000141" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000052", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0002266" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000141", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0010000" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000141", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0010001" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001018", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000125" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001241", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000051" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001241", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001018" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001241", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001995" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001992", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001993" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001995", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001992" - }, { "obj": "http://purl.obolibrary.org/obo/RO_0000052", "pred": "subPropertyOf", @@ -1361,9 +1221,9 @@ "sub": "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007" }, { - "obj": "http://www.w3.org/2002/07/owl#topObjectProperty", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002131" + "obj": "http://www.w3.org/2002/07/owl#Thing", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/BFO_0000001" }, { "obj": "http://xmlns.com/foaf/0.1/image", @@ -1376,62 +1236,9 @@ "sub": "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014" } ], - "equivalentNodesSets": [ - { - "nodeIds": [ - "http://purl.obolibrary.org/obo/CARO_0000013", - "http://purl.obolibrary.org/obo/CL_0000003" - ] - }, - { - "nodeIds": [ - "http://purl.obolibrary.org/obo/CARO_0010004", - "http://purl.obolibrary.org/obo/NCBITaxon_131567" - ] - } - ], + "equivalentNodesSets": [], "id": "http://purl.obolibrary.org/obo/vfbext/vfbext-non-classified.json", "logicalDefinitionAxioms": [ - { - "definedClassId": "http://purl.obolibrary.org/obo/CARO_0000003", - "genusIds": [ - "http://purl.obolibrary.org/obo/CARO_0000006" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0002266", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - }, - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0010000", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - } - ] - }, - { - "definedClassId": "http://purl.obolibrary.org/obo/CARO_0000006", - "genusIds": [ - "http://purl.obolibrary.org/obo/CARO_0000000" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0000125", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - } - ] - }, - { - "definedClassId": "http://purl.obolibrary.org/obo/CARO_0010000", - "genusIds": [ - "http://purl.obolibrary.org/obo/CARO_0000003" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0001993", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - } - ] - }, { "definedClassId": "http://purl.obolibrary.org/obo/FBbt_10000000", "genusIds": [ @@ -1469,11 +1276,11 @@ }, { "pred": "http://purl.org/dc/terms/license", - "val": "https://creativecommons.org/licenses/by/3.0/" + "val": "https://creativecommons.org/licenses/by/4.0/" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:01:2022 13:13" + "val": "25:02:2022 15:21" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -1481,11 +1288,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-01-24" + "val": "2022-02-25" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-01-24/vfbext-non-classified.json", + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/vfbext-non-classified.json", "xrefs": [] }, "nodes": [ @@ -1711,1132 +1518,339 @@ "type": "CLASS" }, { - "id": "http://purl.obolibrary.org/obo/BFO_0000016", - "lbl": "disposition", + "id": "http://purl.obolibrary.org/obo/BFO_0000017", + "lbl": "realizable entity", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000020", + "lbl": "specifically dependent continuant", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000023", + "lbl": "role", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000031", + "lbl": "generically dependent continuant", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000040", + "lbl": "material entity", + "meta": { + "definition": { + "val": "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl": "part_of", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "disposition" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Disposition" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "is part of" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an atom of element X has the disposition to decay to an atom of element Y" + "val": "my brain is part of my body (continuant parthood, two material entities)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "certain people have a predisposition to colon cancer" + "val": "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "children are innately disposed to categorize objects in certain ways." + "val": "this day is part of this year (occurrent parthood)" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." + "val": "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/" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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'." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "part_of" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " + "pred": "http://purl.obolibrary.org/obo/RO_0001900", + "val": "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000017", - "lbl": "realizable entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "realizable" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "RealizableEntity" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the disposition of this piece of metal to conduct electricity." + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000017" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the disposition of your blood to coagulate" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000019" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of your reproductive organs" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000020" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of being a doctor" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000031" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of this boundary to delineate where Utah and Colorado meet" + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "external" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "relationship" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "part_of" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://www.obofoundry.org/ro/#OBO_REL:part_of" } ], "definition": { - "val": "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.", + "val": "a core relation that holds between a part and its whole", "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000019", - "lbl": "quality", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "quality" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Quality" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the ambient temperature of this portion of air" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the color of a tomato" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the length of the circumference of your waist" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the mass of this piece of gold." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the shape of your nose" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the shape of your nostril" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " - }, + }, + "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": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " + "val": "BFO:0000050" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "val": "OBO_REL:part_of" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/BFO_0000020", - "lbl": "specifically dependent continuant", + "id": "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl": "has_part", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "sdc" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "SpecificallyDependentContinuant" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "of one-sided specifically dependent continuants: the mass of this tomato" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the disposition of this fish to decay" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of this heart: to pump blood" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the mutual dependence of proton donors and acceptors in chemical reactions [79" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the pink color of a medium rare piece of grilled filet mignon at its center" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has part" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of being a doctor" + "val": "my body has part my brain (continuant parthood, two material entities)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the shape of this hole." + "val": "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the smell of this portion of mozzarella" + "val": "this year has part this day (occurrent parthood)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "definition": { - "val": "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000023", - "lbl": "role", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "role" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Role" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the priest role" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of a boundary to demarcate two neighboring administrative territories" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of a building in serving as a military target" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of a stone in marking a property boundary" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of subject in a clinical trial" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the student role" + "val": "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." }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000031", - "lbl": "generically dependent continuant", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "gdc" + "val": "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/" }, { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "GenericallyDependentContinuant" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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'." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "has_part" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" + "pred": "http://purl.obolibrary.org/obo/RO_0001900", + "val": "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "external" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "relationship" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "has_part" } ], "definition": { - "val": "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.", + "val": "a core relation that holds between a whole and its part", "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000034", - "lbl": "function", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "function" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Function" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of a hammer to drive in nails" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of a heart pacemaker to regulate the beating of a heart through electricity" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of amylase in saliva to break down starch into sugar" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" - }, + }, + "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": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " + "val": "BFO:0000051" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "val": "OBO_REL:has_part" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/BFO_0000040", - "lbl": "material entity", + "id": "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl": "preceded by", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "material" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "MaterialEntity" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "preceded by" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a flame" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a forest fire" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a human being" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a hurricane" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a photon" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a puff of smoke" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a sea wave" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a tornado" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an aggregate of human beings." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an energy wave" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an epidemic" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the undetached arm of a human being" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "definition": { - "val": "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl": "part_of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "is part of" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my brain is part of my body (continuant parthood, two material entities)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this day is part of this year (occurrent parthood)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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/" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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'." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "part_of" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/BFO" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000002" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000003" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000004" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000017" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000019" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000020" - }, - { - "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": "external" - }, - { - "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" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://www.obofoundry.org/ro/#OBO_REL:part_of" - } - ], - "definition": { - "val": "a core relation that holds between a part and its whole", - "xrefs": [] - }, - "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" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl": "has_part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "has part" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my body has part my brain (continuant parthood, two material entities)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this year has part this day (occurrent parthood)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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/" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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'." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "has_part" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/BFO" - }, - { - "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": "external" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "has_part" - } - ], - "definition": { - "val": "a core relation that holds between a whole and its part", - "xrefs": [] - }, - "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" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl": "preceded by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "is preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "preceded_by" - }, - { - "pred": "http://purl.org/dc/elements/1.1/source", - "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl": "precedes", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "precedes" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000141", - "lbl": "immaterial entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "immaterial" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "ImmaterialEntity" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000000", - "lbl": "anatomical entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/caro.owl" - } - ], - "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." - ], - "definition": { - "val": "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.", - "xrefs": [ - "CAROC:Brownsville2014" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000003", - "lbl": "connected anatomical structure", - "meta": { - "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." - ], - "definition": { - "val": "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000004", - "lbl": "organism substance", - "meta": { - "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." - } - ], - "comments": [ - "Note - CARO explicitly declares organisms substances to be part of (some) organism." - ], - "definition": { - "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.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "portion of organism substance", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000006", - "lbl": "material anatomical entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/caro.owl" - } - ], - "definition": { - "val": "An anatomical entity that has mass.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000007", - "lbl": "immaterial anatomical entity", - "meta": { - "definition": { - "val": "Anatomical entity that has no mass.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000012", - "lbl": "multicellular organism", - "meta": { - "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." - ], - "definition": { - "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000013", - "lbl": "cell", - "meta": { - "comments": [ - "deprecate and replace with CL or GO term?" - ], - "definition": { - "val": "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", - "xrefs": [] - }, - "xrefs": [ - { - "val": "CL:0000000" - }, - { - "val": "GO:0005623" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000014", - "lbl": "cell part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "cell component" - } - ], - "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." - ], - "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000032", - "lbl": "organism subdivision", - "meta": { - "basicPropertyValues": [ - { - "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." - } - ], - "definition": { - "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": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000040", - "lbl": "acellular anatomical structure", - "meta": { - "comments": [ - "Example. Insect cuticle, eggshell, hair." - ], - "definition": { - "val": "An anatomical structure that has no cells or cell parts as a part.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000042", - "lbl": "extraembryonic structure", - "meta": { - "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" - ], - "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#plus" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0001000", - "lbl": "multi-cell-part structure", - "meta": { - "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "multi-cell-component structure" - } - ], - "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." - ], - "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0001008", - "lbl": "gross anatomical part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "mah" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "10.7.2011" - } - ], - "definition": { - "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. ", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#plus" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0001010", - "lbl": "organism or virus or viroid", - "meta": { - "basicPropertyValues": [ + "val": "is preceded by" + }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Melissa Haendel" + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "preceded_by" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "9/18/11" + "pred": "http://purl.org/dc/elements/1.1/source", + "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ], "definition": { - "val": "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.", + "val": "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.", "xrefs": [] - } + }, + "subsets": [ + "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" + ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/CARO_0010000", - "lbl": "multicellular anatomical structure", + "id": "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl": "precedes", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "djs93" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "Sun Feb 27 10:53:00 GMT 2011" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "precedes" } ], "definition": { - "val": "An anatomical structure that has more than one cell as a part.", + "val": "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.", "xrefs": [] }, "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" + "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/CARO_0010004", - "lbl": "cellular organism", + "id": "http://purl.obolibrary.org/obo/CARO_0000000", + "lbl": "anatomical entity", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "mah" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "7.16.2011" + "pred": "http://purl.obolibrary.org/obo/IAO_0000412", + "val": "http://purl.obolibrary.org/obo/caro.owl" } ], "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. " + "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." ], "definition": { - "val": "An individual member of a clade of cellular organisms.", - "xrefs": [] + "val": "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.", + "xrefs": [ + "CAROC:Brownsville2014" + ] } }, "type": "CLASS" }, { - "id": "http://purl.obolibrary.org/obo/CARO_0020000", - "lbl": "disconnected anatomical group", + "id": "http://purl.obolibrary.org/obo/CARO_0000006", + "lbl": "material anatomical entity", "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000412", + "val": "http://purl.obolibrary.org/obo/caro.owl" + } + ], "definition": { - "val": "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", + "val": "An anatomical entity that has mass.", "xrefs": [] }, "subsets": [ @@ -2891,26 +1905,6 @@ }, "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/CL_0000003", - "lbl": "native cell", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/cl.owl" - } - ], - "comments": [ - "To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12)." - ], - "definition": { - "val": "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).", - "xrefs": [] - } - }, - "type": "CLASS" - }, { "id": "http://purl.obolibrary.org/obo/FBbt_00007001", "lbl": "anatomical structure", @@ -3133,60 +2127,94 @@ "type": "CLASS" }, { - "id": "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl": "definition", + "id": "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl": "example of usage", "meta": { "basicPropertyValues": [ { - "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": "uberon" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val": "true" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "example_of_usage" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } + ], + "xrefs": [ + { + "val": "IAO:0000112" + } ] }, "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_10239", - "lbl": "Viruses", + "id": "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl": "definition", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val": "http://purl.obolibrary.org/obo/iao.owl" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_12884", - "lbl": "Viroids", + "id": "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl": "editor note", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" + "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#shorthand", + "val": "editor_note" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val": "http://purl.obolibrary.org/obo/iao.owl" + } + ], + "xrefs": [ + { + "val": "IAO:0000116" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "lbl": "cellular organisms", + "id": "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl": "elucidation", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" + "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val": "http://purl.obolibrary.org/obo/iao.owl" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000293", @@ -3273,33 +2301,7 @@ } ], "definition": { - "val": "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.", - "xrefs": [ - "PATOC:GVG" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "trait", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000051", - "lbl": "morphology", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "quality" - } - ], - "definition": { - "val": "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.", + "val": "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities", "xrefs": [ "PATOC:GVG" ] @@ -3307,104 +2309,6 @@ }, "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000125", - "lbl": "mass", - "meta": { - "definition": { - "val": "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000141", - "lbl": "structure", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "quality" - } - ], - "definition": { - "val": "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.", - "xrefs": [ - "PATOC:GVG" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "relational structural quality", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001241", - "lbl": "physical object quality", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "quality" - } - ], - "definition": { - "val": "A quality which inheres in a continuant.", - "xrefs": [ - "PATOC:GVG" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "monadic quality of a continuant", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "multiply inhering quality of a physical entity ", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of a continuant", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of a single physical entity", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of an object", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of continuant", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "val": "monadic quality of an object", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "val": "monadic quality of continuant", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, { "id": "http://purl.obolibrary.org/obo/RO_0000052", "lbl": "characteristic of", @@ -3456,7 +2360,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0000053", - "lbl": "has_characteristic", + "lbl": "has characteristic", "meta": { "basicPropertyValues": [ { @@ -4145,10 +3049,6 @@ "val": "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ], - "comments": [ - "For use in recording has_part with a cardinality constraint.", - "Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ?" - ], "definition": { "val": "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.", "xrefs": [] @@ -4351,7 +3251,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0002215", - "lbl": "capable of", + "lbl": "capable_of", "meta": { "basicPropertyValues": [ { @@ -6274,6 +5174,21 @@ }, "type": "CLASS" }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000016", + "lbl": "disposition", + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000019", + "lbl": "quality", + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000034", + "lbl": "function", + "type": "CLASS" + }, { "id": "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", "lbl": "has_exemplar", @@ -6299,46 +5214,6 @@ "lbl": "transferase activity, transferring phosphorus-containing groups", "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000052", - "lbl": "shape", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001018", - "lbl": "physical quality", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001992", - "lbl": "cellularity", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001993", - "lbl": "multicellular", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001995", - "lbl": "organismal quality", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0002266", - "lbl": "3-D shape", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0010000", - "lbl": "maximally connected", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0010001", - "lbl": "disconnected", - "type": "CLASS" - }, { "id": "http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0", "lbl": "exemplar_of", @@ -6404,6 +5279,11 @@ "lbl": "database_cross_reference", "type": "PROPERTY" }, + { + "id": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "lbl": "has_obo_namespace", + "type": "PROPERTY" + }, { "id": "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl": "in_subset", diff --git a/vfbext-non-classified.obo b/vfbext-non-classified.obo index d813f03..8be88fd 100644 --- a/vfbext-non-classified.obo +++ b/vfbext-non-classified.obo @@ -1,8 +1,7 @@ format-version: 1.2 -data-version: vfbext/releases/2022-01-24/vfbext-non-classified.owl -date: 24:01:2022 13:13 +data-version: vfbext/releases/2022-02-25/vfbext-non-classified.owl +date: 25:02:2022 15:21 subsetdef: clone "" -subsetdef: core "" subsetdef: cur "" subsetdef: EmbDevSlim "" subsetdef: goslim_aspergillus "" @@ -20,7 +19,6 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: larval_OF "" subsetdef: neuron "" subsetdef: ns_part "" -subsetdef: plus "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: synaptic_neuropil "" @@ -29,20 +27,20 @@ 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/3.0/ xsd:string -property_value: owl:versionInfo "2022-01-24" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string +property_value: owl:versionInfo "2022-02-25" xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string -property_value: IAO:0000112 "Julius Caesar" xsd:string -property_value: IAO:0000112 "the Second World War" xsd:string -property_value: IAO:0000112 "Verdi’s Requiem" xsd:string -property_value: IAO:0000112 "your body mass index" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: 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 @@ -55,8 +53,8 @@ disjoint_from: BFO:0000003 ! occurrent relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string -property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: 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"} @@ -80,21 +78,20 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string -property_value: IAO:0000112 "a chair" xsd:string -property_value: IAO:0000112 "a heart" xsd:string -property_value: IAO:0000112 "a leg" xsd:string -property_value: IAO:0000112 "a molecule" xsd:string -property_value: IAO:0000112 "a spatial region" xsd:string -property_value: IAO:0000112 "an atom" xsd:string -property_value: IAO:0000112 "an orchestra." xsd:string -property_value: IAO:0000112 "an organism" xsd:string -property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string -property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: 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"} @@ -113,18 +110,6 @@ id: BFO:0000016 name: disposition is_a: BFO:0000017 ! realizable entity disjoint_from: BFO:0000023 ! role -property_value: BFO:0000179 "disposition" xsd:string -property_value: BFO:0000180 "Disposition" xsd:string -property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string -property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string -property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string -property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string -property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 @@ -133,152 +118,44 @@ def: "A specifically dependent continuant that inheres in continuant entities is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality relationship: part_of BFO:0000017 ! realizable entity -property_value: BFO:0000179 "realizable" xsd:string -property_value: BFO:0000180 "RealizableEntity" xsd:string -property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string -property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string -property_value: IAO:0000112 "the function of your reproductive organs" xsd:string -property_value: IAO:0000112 "the role of being a doctor" xsd:string -property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string -property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant relationship: part_of BFO:0000019 ! quality -property_value: BFO:0000179 "quality" xsd:string -property_value: BFO:0000180 "Quality" xsd:string -property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string -property_value: IAO:0000112 "the color of a tomato" xsd:string -property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string -property_value: IAO:0000112 "the mass of this piece of gold." xsd:string -property_value: IAO:0000112 "the shape of your nose" xsd:string -property_value: IAO:0000112 "the shape of your nostril" xsd:string -property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} -def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000020 ! specifically dependent continuant -property_value: BFO:0000179 "sdc" xsd:string -property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string -property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string -property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string -property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string -property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string -property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string -property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string -property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string -property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string -property_value: IAO:0000112 "the role of being a doctor" xsd:string -property_value: IAO:0000112 "the shape of this hole." xsd:string -property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} -property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} -property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role def: "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." [] is_a: BFO:0000017 ! realizable entity -property_value: BFO:0000179 "role" xsd:string -property_value: BFO:0000180 "Role" xsd:string -property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string -property_value: IAO:0000112 "the priest role" xsd:string -property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string -property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string -property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string -property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string -property_value: IAO:0000112 "the student role" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string -property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant def: "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." [] -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant relationship: part_of BFO:0000031 ! generically dependent continuant -property_value: BFO:0000179 "gdc" xsd:string -property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string -property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string -property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string -property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string -property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000034 name: function is_a: BFO:0000016 ! disposition -property_value: BFO:0000179 "function" xsd:string -property_value: BFO:0000180 "Function" xsd:string -property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string -property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string -property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000040 name: material entity def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant -disjoint_from: BFO:0000141 ! immaterial entity -property_value: BFO:0000179 "material" xsd:string -property_value: BFO:0000180 "MaterialEntity" xsd:string -property_value: IAO:0000112 "a flame" xsd:string -property_value: IAO:0000112 "a forest fire" xsd:string -property_value: IAO:0000112 "a human being" xsd:string -property_value: IAO:0000112 "a hurricane" xsd:string -property_value: IAO:0000112 "a photon" xsd:string -property_value: IAO:0000112 "a puff of smoke" xsd:string -property_value: IAO:0000112 "a sea wave" xsd:string -property_value: IAO:0000112 "a tornado" xsd:string -property_value: IAO:0000112 "an aggregate of human beings." xsd:string -property_value: IAO:0000112 "an energy wave" xsd:string -property_value: IAO:0000112 "an epidemic" xsd:string -property_value: IAO:0000112 "the undetached arm of a human being" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string -property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000141 -name: immaterial entity -is_a: BFO:0000004 ! independent continuant -property_value: BFO:0000179 "immaterial" xsd:string -property_value: BFO:0000180 "ImmaterialEntity" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: CARO:0000000 @@ -288,26 +165,6 @@ comment: Following BFO, material anatomical entities may have immaterial parts ( is_a: CARO:0030000 ! biological entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl -[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 -intersection_of: CARO:0000006 ! material anatomical entity -intersection_of: has_characteristic PATO:0002266 ! 3-D shape -intersection_of: has_characteristic PATO:0010000 ! maximally connected -disjoint_from: CARO:0000004 ! organism substance - -[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:0000006 ! material anatomical entity -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 @@ -315,150 +172,8 @@ def: "An anatomical entity that has mass." [] subset: core is_a: BFO:0000040 ! material entity is_a: CARO:0000000 ! anatomical entity -intersection_of: CARO:0000000 ! anatomical entity -intersection_of: has_characteristic PATO:0000125 ! mass -disjoint_from: CARO:0000007 ! immaterial anatomical entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl -[Term] -id: CARO:0000007 -name: immaterial anatomical entity -def: "Anatomical entity that has no mass." [] -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 -equivalent_to: CL:0000003 ! native cell -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: part_of CARO:0000013 ! 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. -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 -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 -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: part_of CARO:0000012 ! multicellular organism -property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.7.2011" xsd:string -property_value: IAO:0000117 "mah" xsd:string - -[Term] -id: CARO:0001010 -name: organism or virus or viroid -def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] -is_a: BFO:0000040 ! material entity -union_of: NCBITaxon:10239 ! Viruses -union_of: NCBITaxon:12884 ! Viroids -union_of: NCBITaxon:131567 ! cellular organisms -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 -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: has_characteristic 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"} ! multicellular -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 or virus or viroid -equivalent_to: NCBITaxon:131567 ! cellular organisms -property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string -property_value: IAO:0000117 "mah" xsd:string - -[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 -intersection_of: CARO:0000006 ! material anatomical entity -intersection_of: has_characteristic PATO:0010001 ! disconnected -intersection_of: RO:0002180 CARO:0000003 {minCardinality="2"} ! has component connected anatomical structure - [Term] id: CARO:0020003 name: cellular anatomical structure @@ -479,14 +194,6 @@ 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: has_part CARO:0000013 ! cell - -[Term] -id: CL:0000003 -name: native cell -def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [] -comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). -property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [Term] id: FBbt:00007001 @@ -588,108 +295,15 @@ id: GO:0016772 name: transferase activity, transferring phosphorus-containing groups is_a: GO:0016740 ! transferase activity -[Term] -id: NCBITaxon:10239 -name: Viruses -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - -[Term] -id: NCBITaxon:12884 -name: Viroids -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - -[Term] -id: NCBITaxon:131567 -name: cellular organisms -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -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 property_value: IAO:0000589 "quality (PATO)" xsd:string -[Term] -id: PATO:0000051 -name: morphology -namespace: quality -def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [PATOC:GVG] -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0000052 -name: shape -is_a: PATO:0000051 ! morphology - -[Term] -id: PATO:0000125 -name: mass -def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [] -is_a: PATO:0001018 ! physical quality - -[Term] -id: PATO:0000141 -name: structure -namespace: quality -def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] -synonym: "relational structural quality" EXACT [] -is_a: PATO:0000051 ! morphology - -[Term] -id: PATO:0001018 -name: physical quality -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0001241 -name: physical object quality -namespace: quality -def: "A quality which inheres in a continuant." [PATOC:GVG] -synonym: "monadic quality of a continuant" EXACT [] -synonym: "monadic quality of an object" NARROW [] -synonym: "monadic quality of continuant" NARROW [] -synonym: "multiply inhering quality of a physical entity " EXACT [] -synonym: "quality of a continuant" EXACT [] -synonym: "quality of a single physical entity" EXACT [] -synonym: "quality of an object" EXACT [] -synonym: "quality of continuant" EXACT [] -is_a: PATO:0000001 ! quality - -[Term] -id: PATO:0001992 -name: cellularity -is_a: PATO:0001995 ! organismal quality - -[Term] -id: PATO:0001993 -name: multicellular -is_a: PATO:0001992 ! cellularity - -[Term] -id: PATO:0001995 -name: organismal quality -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0002266 -name: 3-D shape -is_a: PATO:0000052 ! shape - -[Term] -id: PATO:0010000 -name: maximally connected -is_a: PATO:0000141 ! structure - -[Term] -id: PATO:0010001 -name: disconnected -is_a: PATO:0000141 ! structure - [Term] id: VFB:10000005 name: cell cluster @@ -734,9 +348,9 @@ 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: 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 @@ -796,10 +410,10 @@ def: "This relation obtains between an objective specification and a planned pro 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 @@ -809,12 +423,12 @@ 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: 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 @@ -825,8 +439,8 @@ 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: 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: 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:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function @@ -838,8 +452,8 @@ 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: 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: 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:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: characteristic_of ! characteristic_of @@ -850,8 +464,8 @@ 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: 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: 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:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string is_a: characteristic_of ! characteristic_of @@ -861,8 +475,8 @@ inverse_of: RO:0000087 ! has role 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: 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: 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:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function @@ -872,8 +486,8 @@ is_a: has_characteristic ! has_characteristic id: RO:0000086 name: has quality def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: 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:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality is_a: has_characteristic ! has_characteristic @@ -882,8 +496,8 @@ is_a: has_characteristic ! has_characteristic 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: 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: 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:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role @@ -1033,11 +647,9 @@ is_a: BFO:0000063 ! precedes 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." [] -comment: For use in recording has_part with a cardinality constraint. -comment: Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ? 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 @@ -1047,7 +659,7 @@ is_a: has_part ! has part 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: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string +property_value: example_of_usage "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: BFO:0000002 ! continuant @@ -1089,7 +701,7 @@ 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: 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: 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: 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 @@ -1100,7 +712,7 @@ 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: 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: 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: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -1129,7 +741,7 @@ 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: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 @@ -1151,7 +763,7 @@ property_value: RO:0001900 RO:0001901 id: RO:0002327 name: enables subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string @@ -1243,7 +855,7 @@ 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: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: example_of_usage "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 @@ -1292,8 +904,8 @@ inverse_of: RO:0002412 ! immediately causally upstream of id: RO:0002410 name: causally related to def: "This relation groups causal relations between material entities and causal relations between processes" [] +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:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -1324,7 +936,7 @@ id: RO:0002418 name: causally upstream of or within def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] synonym: "affects" RELATED [] -property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true @@ -1375,7 +987,7 @@ 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: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -1389,8 +1001,8 @@ 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: 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: 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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI @@ -1413,7 +1025,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: editor_note "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with @@ -1494,7 +1106,7 @@ property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: 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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -1555,7 +1167,7 @@ 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: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: example_of_usage "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: has_part capable_of is_a: RO:0002328 ! functionally related to @@ -1565,7 +1177,7 @@ 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: 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: 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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity @@ -1576,7 +1188,7 @@ 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: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: example_of_usage "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -1593,7 +1205,7 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: example_of_usage "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 positively_regulates is_a: RO:0002596 ! capable of regulating @@ -1716,7 +1328,7 @@ is_a: RO:0002566 ! causally influences id: RO:0017001 name: utilizes def: "X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y." [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string +property_value: example_of_usage "A diagnostic testing device utilizes a specimen." xsd:string property_value: IAO:0000117 "Asiyah Lin" xsd:string property_value: IAO:0000117 "https://orcid.org/0000-0001-9625-1899 Bill Duncan" xsd:string 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 @@ -1790,8 +1402,8 @@ 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: 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: 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 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 @@ -1823,15 +1435,31 @@ 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: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: has_characteristic ! has_characteristic +[Typedef] +id: editor_note +name: editor note +namespace: uberon +xref: IAO:0000116 +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + +[Typedef] +id: example_of_usage +name: example of usage +namespace: uberon +xref: IAO:0000112 +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + [Typedef] id: expresses name: expresses @@ -1849,10 +1477,10 @@ 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: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 @@ -1871,15 +1499,14 @@ 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: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: IAO:0000412 http://purl.obolibrary.org/obo/BFO property_value: RO:0001900 RO:0001901 is_transitive: true is_a: overlaps ! overlaps @@ -1945,15 +1572,14 @@ 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: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: IAO:0000412 http://purl.obolibrary.org/obo/BFO property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 @@ -1997,8 +1623,8 @@ 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: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string diff --git a/vfbext-non-classified.owl b/vfbext-non-classified.owl index 4d12403..f72184c 100644 --- a/vfbext-non-classified.owl +++ b/vfbext-non-classified.owl @@ -9,7 +9,6 @@ xmlns:vfb="http://purl.obolibrary.org/obo/fbbt/vfb#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:caro="http://purl.obolibrary.org/obo/caro#" xmlns:fbbt="http://purl.obolibrary.org/obo/fbbt#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" @@ -22,13 +21,13 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:oboInOwl2="ttp://www.geneontology.org/formats/oboInOwl#"> - + An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology - https://creativecommons.org/licenses/by/3.0/</terms:license> - 24:01:2022 13:13 + https://creativecommons.org/licenses/by/4.0/</terms:license> + 25:02:2022 15:21 VFB extension ontology - 2022-01-24 + 2022-02-25 @@ -64,7 +63,16 @@ - + + IAO:0000112 + uberon + example_of_usage + true + example_of_usage + + example of usage + example of usage + @@ -87,7 +95,16 @@ - + + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + editor note + @@ -135,7 +152,10 @@ - + + + elucidation + @@ -157,12 +177,6 @@ - - - - - - @@ -251,22 +265,6 @@ - - - - - - - - - - - - - - - - @@ -511,15 +509,11 @@ - - - - - - - + + has_obo_namespace + @@ -543,6 +537,12 @@ + + + + + + @@ -555,6 +555,12 @@ + + + + + + @@ -601,7 +607,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of - @@ -646,7 +651,6 @@ 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 @@ -1238,7 +1242,6 @@ Examples include: the relationship between two channels collected simultaneously - @@ -1247,10 +1250,6 @@ Examples include: the relationship between two channels collected simultaneously - - - - @@ -1295,8 +1294,6 @@ Examples include: the relationship between two channels collected simultaneously 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. - For use in recording has_part with a cardinality constraint. - Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ? has component @@ -2709,6 +2706,7 @@ For example, A and B may be gene products and binding of B by A positively regul + entity Entity Julius Caesar @@ -2937,44 +2935,8 @@ For example, A and B may be gene products and binding of B by A positively regul - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - disposition - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - @@ -2989,45 +2951,9 @@ For example, A and B may be gene products and binding of B by A positively regul - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet 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. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - realizable entity - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - @@ -3041,45 +2967,8 @@ For example, A and B may be gene products and binding of B by A positively regul - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - quality - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - @@ -3094,59 +2983,9 @@ For example, A and B may be gene products and binding of B by A positively regul - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - specifically dependent continuant - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - @@ -3154,34 +2993,9 @@ For example, A and B may be gene products and binding of B by A positively regul - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role 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. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - role - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - @@ -3195,29 +3009,9 @@ For example, A and B may be gene products and binding of B by A positively regul - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - generically dependent continuant - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - @@ -3225,29 +3019,8 @@ For example, A and B may be gene products and binding of B by A positively regul - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - function - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - @@ -3255,83 +3028,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - material entity - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - @@ -3339,10 +3038,6 @@ 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 @@ -3359,70 +3054,11 @@ 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 - - - - - - - - - - - - - - - - - - - - - - An anatomical entity that has mass. CARO:0000006 @@ -3433,362 +3069,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - Anatomical entity that has no mass. - CARO:0000007 - - immaterial anatomical entity - - - - - - - - - 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 - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 - - - - - - - - - - - - - - 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 - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - 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 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. - mah - 10.7.2011 - - gross anatomical part - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - An individual member of a clade of cellular organisms. - mah - 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 - - - - - - - - - - - - - - - - - - 2 - - - - - - Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. - CARO:0000054 - - disconnected anatomical group - - - - - - - - - - - - - - - An anatomical structure consisting of one or more cells. 2018-09-28T14:20:19Z cellular anatomical structure dos - - - - - - - - - - - - - - - With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell - @@ -3807,29 +3096,12 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. expression pattern - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - @@ -3847,7 +3119,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process 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 + CARO:MAH FBC:DOS @@ -3926,7 +3198,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process Anatomical entity which is part_of Drosophila melanogaster. - CARO:MAH + CARO:MAH @@ -4020,33 +3292,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - Viruses - - - - - - - - - Viroids - - - - - - - - - cellular organisms - - - - @@ -4058,10 +3303,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process 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. quality (PATO) PATO:0000072 - trait quality PATO:0000001 quality @@ -4072,158 +3315,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process 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 quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - quality - PATO:0000051 - morphology - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - PATOC:GVG - - - - - - - - - shape - - - - - - - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - PATO:0000125 - mass - - - - - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - relational structural quality - quality - PATO:0000141 - structure - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATOC:GVG - - - - - - - - - physical quality - - - - - - - - - A quality which inheres in a continuant. - monadic quality of a continuant - multiply inhering quality of a physical entity - quality of a continuant - quality of a single physical entity - quality of an object - quality of continuant - monadic quality of an object - monadic quality of continuant - quality - PATO:0001241 - physical object quality - - - - - A quality which inheres in a continuant. - PATOC:GVG - - - - - - - - - cellularity - - - - - - - - - multicellular - - - - - - - - - organismal quality - - - - - - - - - 3-D shape - - - - - - - - - maximally connected - - - - - - - - - disconnected - @@ -4313,33 +3404,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - Should belong in BFO, but lives in caro for now. - @@ -4373,22 +3437,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - - - - - - diff --git a/vfbext-simple.json b/vfbext-simple.json index c04b917..7516915 100644 --- a/vfbext-simple.json +++ b/vfbext-simple.json @@ -56,11 +56,11 @@ }, { "pred": "http://purl.org/dc/terms/license", - "val": "https://creativecommons.org/licenses/by/3.0/" + "val": "https://creativecommons.org/licenses/by/4.0/" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:01:2022 13:14" + "val": "25:02:2022 15:22" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -68,11 +68,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-01-24" + "val": "2022-02-25" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-01-24/vfbext-simple.json", + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/vfbext-simple.json", "xrefs": [] }, "nodes": [ @@ -113,10 +113,6 @@ "pred": "http://purl.obolibrary.org/obo/IAO_0000118", "val": "part_of" }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/BFO" - }, { "pred": "http://purl.obolibrary.org/obo/RO_0001900", "val": "http://purl.obolibrary.org/obo/RO_0001901" diff --git a/vfbext-simple.obo b/vfbext-simple.obo index 42d3ee7..aa270a6 100644 --- a/vfbext-simple.obo +++ b/vfbext-simple.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: vfbext/releases/2022-01-24/vfbext-simple.owl -date: 24:01:2022 13:14 +data-version: vfbext/releases/2022-02-25/vfbext-simple.owl +date: 25:02:2022 15:22 subsetdef: clone "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -14,8 +14,8 @@ remark: VFB extension ontology 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/3.0/ xsd:string -property_value: owl:versionInfo "2022-01-24" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string +property_value: owl:versionInfo "2022-02-25" xsd:string [Term] id: VFB:10000005 @@ -134,7 +134,6 @@ property_value: IAO:0000116 "Everything is part of itself. Any part of any part 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: IAO:0000412 http://purl.obolibrary.org/obo/BFO property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 diff --git a/vfbext-simple.owl b/vfbext-simple.owl index 7ee68ca..4b37761 100644 --- a/vfbext-simple.owl +++ b/vfbext-simple.owl @@ -13,13 +13,13 @@ xmlns:terms="http://purl.org/dc/terms/" 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/3.0/</terms:license> - 24:01:2022 13:14 + https://creativecommons.org/licenses/by/4.0/</terms:license> + 25:02:2022 15:22 VFB extension ontology - 2022-01-24 + 2022-02-25 @@ -88,12 +88,6 @@ - - - - - - @@ -302,7 +296,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of - diff --git a/vfbext.json b/vfbext.json index 211e567..3e62f7b 100644 --- a/vfbext.json +++ b/vfbext.json @@ -335,11 +335,6 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/BFO_0000040" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000004", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/BFO_0000141" - }, { "obj": "http://purl.obolibrary.org/obo/BFO_0000004", "pred": "is_a", @@ -395,11 +390,6 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/CARO_0000006" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000040", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0001010" - }, { "obj": "http://purl.obolibrary.org/obo/BFO_0000050", "pred": "subPropertyOf", @@ -445,141 +435,21 @@ "pred": "subPropertyOf", "sub": "http://purl.obolibrary.org/obo/RO_0002411" }, - { - "obj": "http://purl.obolibrary.org/obo/BFO_0000141", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000007" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000000", "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/CARO_0000006" }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000000", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000007" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000000", "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/FBbt_10000000" }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "http://purl.obolibrary.org/obo/RO_0002180", - "sub": "http://purl.obolibrary.org/obo/CARO_0020000" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000014" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000040" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000042" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0010000" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000006", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000003" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000006", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0001008" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000006", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0020000" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0000006", "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/CARO_0020003" }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000012", - "pred": "http://purl.obolibrary.org/obo/BFO_0000050", - "sub": "http://purl.obolibrary.org/obo/CARO_0001008" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000013", - "pred": "http://purl.obolibrary.org/obo/BFO_0000050", - "sub": "http://purl.obolibrary.org/obo/CARO_0000014" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000013", - "pred": "http://purl.obolibrary.org/obo/BFO_0000051", - "sub": "http://purl.obolibrary.org/obo/CARO_0030002" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0000013", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CL_0000003" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000004" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000040" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000042" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0001000" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001008", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0010000" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001010", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/NCBITaxon_10239" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0001010", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/NCBITaxon_12884" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0010000", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000032" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0010004", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000012" - }, - { - "obj": "http://purl.obolibrary.org/obo/CARO_0010004", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/NCBITaxon_131567" - }, { "obj": "http://purl.obolibrary.org/obo/CARO_0020003", "pred": "is_a", @@ -595,11 +465,6 @@ "pred": "http://purl.obolibrary.org/obo/BFO_0000050", "sub": "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004" }, - { - "obj": "http://purl.obolibrary.org/obo/CL_0000003", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000013" - }, { "obj": "http://purl.obolibrary.org/obo/FBbt_00007001", "pred": "is_a", @@ -645,106 +510,11 @@ "pred": "is_a", "sub": "http://purl.obolibrary.org/obo/GO_0016301" }, - { - "obj": "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0000012" - }, - { - "obj": "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/CARO_0010004" - }, { "obj": "http://purl.obolibrary.org/obo/NCBITaxon_7227", "pred": "http://purl.obolibrary.org/obo/BFO_0000050", "sub": "http://purl.obolibrary.org/obo/FBbt_10000000" }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000001", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001241" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000051", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000052" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000051", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000141" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000052", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0002266" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000125", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0000006" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000141", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0010000" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0000141", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0010001" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001018", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000125" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001241", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0000051" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001241", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001018" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001241", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001995" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001992", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001993" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001993", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0010000" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0001995", - "pred": "is_a", - "sub": "http://purl.obolibrary.org/obo/PATO_0001992" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0002266", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0000003" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0010000", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0000003" - }, - { - "obj": "http://purl.obolibrary.org/obo/PATO_0010001", - "pred": "http://purl.obolibrary.org/obo/RO_0000053", - "sub": "http://purl.obolibrary.org/obo/CARO_0020000" - }, { "obj": "http://purl.obolibrary.org/obo/RO_0000052", "pred": "subPropertyOf", @@ -1461,9 +1231,9 @@ "sub": "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000007" }, { - "obj": "http://www.w3.org/2002/07/owl#topObjectProperty", - "pred": "subPropertyOf", - "sub": "http://purl.obolibrary.org/obo/RO_0002131" + "obj": "http://www.w3.org/2002/07/owl#Thing", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/BFO_0000001" }, { "obj": "http://xmlns.com/foaf/0.1/image", @@ -1476,62 +1246,9 @@ "sub": "http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000014" } ], - "equivalentNodesSets": [ - { - "nodeIds": [ - "http://purl.obolibrary.org/obo/CARO_0000013", - "http://purl.obolibrary.org/obo/CL_0000003" - ] - }, - { - "nodeIds": [ - "http://purl.obolibrary.org/obo/CARO_0010004", - "http://purl.obolibrary.org/obo/NCBITaxon_131567" - ] - } - ], + "equivalentNodesSets": [], "id": "http://purl.obolibrary.org/obo/vfbext.json", "logicalDefinitionAxioms": [ - { - "definedClassId": "http://purl.obolibrary.org/obo/CARO_0000003", - "genusIds": [ - "http://purl.obolibrary.org/obo/CARO_0000006" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0002266", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - }, - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0010000", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - } - ] - }, - { - "definedClassId": "http://purl.obolibrary.org/obo/CARO_0000006", - "genusIds": [ - "http://purl.obolibrary.org/obo/CARO_0000000" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0000125", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - } - ] - }, - { - "definedClassId": "http://purl.obolibrary.org/obo/CARO_0010000", - "genusIds": [ - "http://purl.obolibrary.org/obo/CARO_0000003" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/PATO_0001993", - "propertyId": "http://purl.obolibrary.org/obo/RO_0000053" - } - ] - }, { "definedClassId": "http://purl.obolibrary.org/obo/FBbt_10000000", "genusIds": [ @@ -1569,11 +1286,11 @@ }, { "pred": "http://purl.org/dc/terms/license", - "val": "https://creativecommons.org/licenses/by/3.0/" + "val": "https://creativecommons.org/licenses/by/4.0/" }, { "pred": "http://www.geneontology.org/formats/oboInOwl#date", - "val": "24:01:2022 13:12" + "val": "25:02:2022 15:21" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -1581,11 +1298,11 @@ }, { "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-01-24" + "val": "2022-02-25" } ], "subsets": [], - "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-01-24/vfbext.json", + "version": "http://purl.obolibrary.org/obo/vfbext/releases/2022-02-25/vfbext.json", "xrefs": [] }, "nodes": [ @@ -1811,1132 +1528,339 @@ "type": "CLASS" }, { - "id": "http://purl.obolibrary.org/obo/BFO_0000016", - "lbl": "disposition", + "id": "http://purl.obolibrary.org/obo/BFO_0000017", + "lbl": "realizable entity", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000020", + "lbl": "specifically dependent continuant", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000023", + "lbl": "role", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000031", + "lbl": "generically dependent continuant", + "meta": { + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000040", + "lbl": "material entity", + "meta": { + "definition": { + "val": "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl": "part_of", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "disposition" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "is part of" }, { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Disposition" + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "my brain is part of my body (continuant parthood, two material entities)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an atom of element X has the disposition to decay to an atom of element Y" + "val": "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "certain people have a predisposition to colon cancer" + "val": "this day is part of this year (occurrent parthood)" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "children are innately disposed to categorize objects in certain ways." + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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/" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." + "val": "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'." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "part_of" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" + "pred": "http://purl.obolibrary.org/obo/RO_0001900", + "val": "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000017", - "lbl": "realizable entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "realizable" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "RealizableEntity" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000004" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the disposition of this piece of metal to conduct electricity." + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000017" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the disposition of your blood to coagulate" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000019" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of your reproductive organs" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000020" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of being a doctor" + "pred": "http://purl.obolibrary.org/obo/RO_0040042", + "val": "http://purl.obolibrary.org/obo/BFO_0000031" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of this boundary to delineate where Utah and Colorado meet" + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "external" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "relationship" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "part_of" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://www.obofoundry.org/ro/#OBO_REL:part_of" } ], "definition": { - "val": "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.", + "val": "a core relation that holds between a part and its whole", "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000019", - "lbl": "quality", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "quality" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Quality" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the ambient temperature of this portion of air" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the color of a tomato" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the length of the circumference of your waist" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the mass of this piece of gold." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the shape of your nose" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the shape of your nostril" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " - }, + }, + "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": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " + "val": "BFO:0000050" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "val": "OBO_REL:part_of" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/BFO_0000020", - "lbl": "specifically dependent continuant", + "id": "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl": "has_part", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "sdc" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "SpecificallyDependentContinuant" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "of one-sided specifically dependent continuants: the mass of this tomato" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the disposition of this fish to decay" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has part" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of this heart: to pump blood" + "val": "my body has part my brain (continuant parthood, two material entities)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the mutual dependence of proton donors and acceptors in chemical reactions [79" + "val": "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" }, { "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" + "val": "this year has part this day (occurrent parthood)" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the pink color of a medium rare piece of grilled filet mignon at its center" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of being a doctor" + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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/" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the shape of this hole." + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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'." }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the smell of this portion of mozzarella" + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "has_part" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." + "pred": "http://purl.obolibrary.org/obo/RO_0001900", + "val": "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "external" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " + "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val": "relationship" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "has_part" } ], "definition": { - "val": "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])", + "val": "a core relation that holds between a whole and its part", "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000023", - "lbl": "role", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "role" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Role" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the priest role" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of a boundary to demarcate two neighboring administrative territories" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of a building in serving as a military target" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of a stone in marking a property boundary" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the role of subject in a clinical trial" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the student role" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" - }, + }, + "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": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " + "val": "BFO:0000051" }, { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" + "val": "OBO_REL:has_part" } - ], - "definition": { - "val": "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.", - "xrefs": [] - } + ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/BFO_0000031", - "lbl": "generically dependent continuant", + "id": "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl": "preceded by", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "gdc" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "GenericallyDependentContinuant" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "preceded by" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000034", - "lbl": "function", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "function" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "Function" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of a hammer to drive in nails" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of a heart pacemaker to regulate the beating of a heart through electricity" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the function of amylase in saliva to break down starch into sugar" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000040", - "lbl": "material entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "material" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "MaterialEntity" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a flame" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a forest fire" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a human being" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a hurricane" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a photon" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a puff of smoke" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a sea wave" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a tornado" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an aggregate of human beings." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an energy wave" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "an epidemic" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "the undetached arm of a human being" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000601", - "val": "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000602", - "val": "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "definition": { - "val": "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl": "part_of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "is part of" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my brain is part of my body (continuant parthood, two material entities)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this day is part of this year (occurrent parthood)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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/" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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'." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "part_of" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/BFO" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000002" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000003" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000004" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000017" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000019" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000020" - }, - { - "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": "external" - }, - { - "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" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://www.obofoundry.org/ro/#OBO_REL:part_of" - } - ], - "definition": { - "val": "a core relation that holds between a part and its whole", - "xrefs": [] - }, - "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" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl": "has_part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "has part" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my body has part my brain (continuant parthood, two material entities)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this year has part this day (occurrent parthood)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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/" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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'." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "has_part" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/BFO" - }, - { - "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": "external" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "relationship" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "has_part" - } - ], - "definition": { - "val": "a core relation that holds between a whole and its part", - "xrefs": [] - }, - "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" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl": "preceded by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "is preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "preceded_by" - }, - { - "pred": "http://purl.org/dc/elements/1.1/source", - "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl": "precedes", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "precedes" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000141", - "lbl": "immaterial entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000179", - "val": "immaterial" - }, - { - "pred": "http://purl.obolibrary.org/obo/BFO_0000180", - "val": "ImmaterialEntity" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000000", - "lbl": "anatomical entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/caro.owl" - } - ], - "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." - ], - "definition": { - "val": "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.", - "xrefs": [ - "CAROC:Brownsville2014" - ] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000003", - "lbl": "connected anatomical structure", - "meta": { - "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." - ], - "definition": { - "val": "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000004", - "lbl": "organism substance", - "meta": { - "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." - } - ], - "comments": [ - "Note - CARO explicitly declares organisms substances to be part of (some) organism." - ], - "definition": { - "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.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "portion of organism substance", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000006", - "lbl": "material anatomical entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/caro.owl" - } - ], - "definition": { - "val": "An anatomical entity that has mass.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000007", - "lbl": "immaterial anatomical entity", - "meta": { - "definition": { - "val": "Anatomical entity that has no mass.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000012", - "lbl": "multicellular organism", - "meta": { - "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." - ], - "definition": { - "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000013", - "lbl": "cell", - "meta": { - "comments": [ - "deprecate and replace with CL or GO term?" - ], - "definition": { - "val": "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", - "xrefs": [] - }, - "xrefs": [ - { - "val": "CL:0000000" - }, - { - "val": "GO:0005623" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000014", - "lbl": "cell part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "cell component" - } - ], - "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." - ], - "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000032", - "lbl": "organism subdivision", - "meta": { - "basicPropertyValues": [ - { - "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." - } - ], - "definition": { - "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": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000040", - "lbl": "acellular anatomical structure", - "meta": { - "comments": [ - "Example. Insect cuticle, eggshell, hair." - ], - "definition": { - "val": "An anatomical structure that has no cells or cell parts as a part.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000042", - "lbl": "extraembryonic structure", - "meta": { - "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" - ], - "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#plus" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0001000", - "lbl": "multi-cell-part structure", - "meta": { - "basicPropertyValues": [ { "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "multi-cell-component structure" - } - ], - "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." - ], - "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0001008", - "lbl": "gross anatomical part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "mah" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "10.7.2011" - } - ], - "definition": { - "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. ", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/caro#plus" - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0001010", - "lbl": "organism or virus or viroid", - "meta": { - "basicPropertyValues": [ + "val": "is preceded by" + }, { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Melissa Haendel" + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "preceded_by" }, { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "9/18/11" + "pred": "http://purl.org/dc/elements/1.1/source", + "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ], "definition": { - "val": "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.", + "val": "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.", "xrefs": [] - } + }, + "subsets": [ + "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" + ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/CARO_0010000", - "lbl": "multicellular anatomical structure", + "id": "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl": "precedes", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "djs93" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "Sun Feb 27 10:53:00 GMT 2011" + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "precedes" } ], "definition": { - "val": "An anatomical structure that has more than one cell as a part.", + "val": "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.", "xrefs": [] }, "subsets": [ - "http://purl.obolibrary.org/obo/caro#core" + "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/CARO_0010004", - "lbl": "cellular organism", + "id": "http://purl.obolibrary.org/obo/CARO_0000000", + "lbl": "anatomical entity", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "mah" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_creation_date", - "val": "7.16.2011" + "pred": "http://purl.obolibrary.org/obo/IAO_0000412", + "val": "http://purl.obolibrary.org/obo/caro.owl" } ], "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. " + "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." ], "definition": { - "val": "An individual member of a clade of cellular organisms.", - "xrefs": [] + "val": "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.", + "xrefs": [ + "CAROC:Brownsville2014" + ] } }, "type": "CLASS" }, { - "id": "http://purl.obolibrary.org/obo/CARO_0020000", - "lbl": "disconnected anatomical group", + "id": "http://purl.obolibrary.org/obo/CARO_0000006", + "lbl": "material anatomical entity", "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000412", + "val": "http://purl.obolibrary.org/obo/caro.owl" + } + ], "definition": { - "val": "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", + "val": "An anatomical entity that has mass.", "xrefs": [] }, "subsets": [ @@ -2991,26 +1915,6 @@ }, "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/CL_0000003", - "lbl": "native cell", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/cl.owl" - } - ], - "comments": [ - "To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12)." - ], - "definition": { - "val": "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).", - "xrefs": [] - } - }, - "type": "CLASS" - }, { "id": "http://purl.obolibrary.org/obo/FBbt_00007001", "lbl": "anatomical structure", @@ -3233,60 +2137,94 @@ "type": "CLASS" }, { - "id": "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl": "definition", + "id": "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl": "example of usage", "meta": { "basicPropertyValues": [ { - "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": "uberon" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val": "true" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val": "example_of_usage" }, { "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val": "http://purl.obolibrary.org/obo/iao.owl" } + ], + "xrefs": [ + { + "val": "IAO:0000112" + } ] }, "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_10239", - "lbl": "Viruses", + "id": "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl": "definition", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val": "http://purl.obolibrary.org/obo/iao.owl" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_12884", - "lbl": "Viroids", + "id": "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl": "editor note", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" + "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#shorthand", + "val": "editor_note" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val": "http://purl.obolibrary.org/obo/iao.owl" + } + ], + "xrefs": [ + { + "val": "IAO:0000116" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_131567", - "lbl": "cellular organisms", + "id": "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl": "elucidation", "meta": { "basicPropertyValues": [ { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/ncbitaxon.owl" + "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val": "http://purl.obolibrary.org/obo/iao.owl" } ] }, - "type": "CLASS" + "type": "PROPERTY" }, { "id": "http://purl.obolibrary.org/obo/OBI_0000293", @@ -3373,33 +2311,7 @@ } ], "definition": { - "val": "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.", - "xrefs": [ - "PATOC:GVG" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "trait", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000051", - "lbl": "morphology", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "quality" - } - ], - "definition": { - "val": "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.", + "val": "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities", "xrefs": [ "PATOC:GVG" ] @@ -3407,104 +2319,6 @@ }, "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000125", - "lbl": "mass", - "meta": { - "definition": { - "val": "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000141", - "lbl": "structure", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "quality" - } - ], - "definition": { - "val": "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.", - "xrefs": [ - "PATOC:GVG" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "relational structural quality", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001241", - "lbl": "physical object quality", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "quality" - } - ], - "definition": { - "val": "A quality which inheres in a continuant.", - "xrefs": [ - "PATOC:GVG" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "monadic quality of a continuant", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "multiply inhering quality of a physical entity ", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of a continuant", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of a single physical entity", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of an object", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "quality of continuant", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "val": "monadic quality of an object", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "val": "monadic quality of continuant", - "xrefs": [] - } - ] - }, - "type": "CLASS" - }, { "id": "http://purl.obolibrary.org/obo/RO_0000052", "lbl": "characteristic of", @@ -3556,7 +2370,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0000053", - "lbl": "has_characteristic", + "lbl": "has characteristic", "meta": { "basicPropertyValues": [ { @@ -4245,10 +3059,6 @@ "val": "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ], - "comments": [ - "For use in recording has_part with a cardinality constraint.", - "Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ?" - ], "definition": { "val": "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.", "xrefs": [] @@ -4451,7 +3261,7 @@ }, { "id": "http://purl.obolibrary.org/obo/RO_0002215", - "lbl": "capable of", + "lbl": "capable_of", "meta": { "basicPropertyValues": [ { @@ -6374,6 +5184,21 @@ }, "type": "CLASS" }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000016", + "lbl": "disposition", + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000019", + "lbl": "quality", + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/BFO_0000034", + "lbl": "function", + "type": "CLASS" + }, { "id": "http://purl.obolibrary.org/obo/C888C3DB-AEFA-447F-BD4C-858DFE33DBE7", "lbl": "has_exemplar", @@ -6399,46 +5224,6 @@ "lbl": "transferase activity, transferring phosphorus-containing groups", "type": "CLASS" }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0000052", - "lbl": "shape", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001018", - "lbl": "physical quality", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001992", - "lbl": "cellularity", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001993", - "lbl": "multicellular", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0001995", - "lbl": "organismal quality", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0002266", - "lbl": "3-D shape", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0010000", - "lbl": "maximally connected", - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/PATO_0010001", - "lbl": "disconnected", - "type": "CLASS" - }, { "id": "http://purl.obolibrary.org/obo/c099d9d6-4ef3-11e3-9da7-b1ad5291e0b0", "lbl": "exemplar_of", @@ -6504,6 +5289,11 @@ "lbl": "database_cross_reference", "type": "PROPERTY" }, + { + "id": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "lbl": "has_obo_namespace", + "type": "PROPERTY" + }, { "id": "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl": "in_subset", diff --git a/vfbext.obo b/vfbext.obo index 119a09d..e23d573 100644 --- a/vfbext.obo +++ b/vfbext.obo @@ -1,7 +1,6 @@ format-version: 1.2 -date: 24:01:2022 13:12 +date: 25:02:2022 15:21 subsetdef: clone "" -subsetdef: core "" subsetdef: cur "" subsetdef: EmbDevSlim "" subsetdef: goslim_aspergillus "" @@ -19,7 +18,6 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: larval_OF "" subsetdef: neuron "" subsetdef: ns_part "" -subsetdef: plus "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: synaptic_neuropil "" @@ -28,20 +26,20 @@ 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/3.0/ xsd:string -property_value: owl:versionInfo "2022-01-24" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ xsd:string +property_value: owl:versionInfo "2022-02-25" xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string -property_value: IAO:0000112 "Julius Caesar" xsd:string -property_value: IAO:0000112 "the Second World War" xsd:string -property_value: IAO:0000112 "Verdi’s Requiem" xsd:string -property_value: IAO:0000112 "your body mass index" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: 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 @@ -54,8 +52,8 @@ disjoint_from: BFO:0000003 ! occurrent relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string -property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: 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"} @@ -79,21 +77,20 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string -property_value: IAO:0000112 "a chair" xsd:string -property_value: IAO:0000112 "a heart" xsd:string -property_value: IAO:0000112 "a leg" xsd:string -property_value: IAO:0000112 "a molecule" xsd:string -property_value: IAO:0000112 "a spatial region" xsd:string -property_value: IAO:0000112 "an atom" xsd:string -property_value: IAO:0000112 "an orchestra." xsd:string -property_value: IAO:0000112 "an organism" xsd:string -property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string -property_value: IAO:0000112 "the interior of your mouth" xsd:string +property_value: 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"} @@ -112,18 +109,6 @@ id: BFO:0000016 name: disposition is_a: BFO:0000017 ! realizable entity disjoint_from: BFO:0000023 ! role -property_value: BFO:0000179 "disposition" xsd:string -property_value: BFO:0000180 "Disposition" xsd:string -property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string -property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string -property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string -property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string -property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000017 @@ -132,152 +117,44 @@ def: "A specifically dependent continuant that inheres in continuant entities is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality relationship: part_of BFO:0000017 ! realizable entity -property_value: BFO:0000179 "realizable" xsd:string -property_value: BFO:0000180 "RealizableEntity" xsd:string -property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string -property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string -property_value: IAO:0000112 "the function of your reproductive organs" xsd:string -property_value: IAO:0000112 "the role of being a doctor" xsd:string -property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string -property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant relationship: part_of BFO:0000019 ! quality -property_value: BFO:0000179 "quality" xsd:string -property_value: BFO:0000180 "Quality" xsd:string -property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string -property_value: IAO:0000112 "the color of a tomato" xsd:string -property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string -property_value: IAO:0000112 "the mass of this piece of gold." xsd:string -property_value: IAO:0000112 "the shape of your nose" xsd:string -property_value: IAO:0000112 "the shape of your nostril" xsd:string -property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} -def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: part_of BFO:0000020 ! specifically dependent continuant -property_value: BFO:0000179 "sdc" xsd:string -property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string -property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string -property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string -property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string -property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string -property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string -property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string -property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string -property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string -property_value: IAO:0000112 "the role of being a doctor" xsd:string -property_value: IAO:0000112 "the shape of this hole." xsd:string -property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} -property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} -property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role def: "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." [] is_a: BFO:0000017 ! realizable entity -property_value: BFO:0000179 "role" xsd:string -property_value: BFO:0000180 "Role" xsd:string -property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string -property_value: IAO:0000112 "the priest role" xsd:string -property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string -property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string -property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string -property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string -property_value: IAO:0000112 "the student role" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string -property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant def: "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." [] -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant relationship: part_of BFO:0000031 ! generically dependent continuant -property_value: BFO:0000179 "gdc" xsd:string -property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string -property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string -property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string -property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string -property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000034 name: function is_a: BFO:0000016 ! disposition -property_value: BFO:0000179 "function" xsd:string -property_value: BFO:0000180 "Function" xsd:string -property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string -property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string -property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000040 name: material entity def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant -disjoint_from: BFO:0000141 ! immaterial entity -property_value: BFO:0000179 "material" xsd:string -property_value: BFO:0000180 "MaterialEntity" xsd:string -property_value: IAO:0000112 "a flame" xsd:string -property_value: IAO:0000112 "a forest fire" xsd:string -property_value: IAO:0000112 "a human being" xsd:string -property_value: IAO:0000112 "a hurricane" xsd:string -property_value: IAO:0000112 "a photon" xsd:string -property_value: IAO:0000112 "a puff of smoke" xsd:string -property_value: IAO:0000112 "a sea wave" xsd:string -property_value: IAO:0000112 "a tornado" xsd:string -property_value: IAO:0000112 "an aggregate of human beings." xsd:string -property_value: IAO:0000112 "an energy wave" xsd:string -property_value: IAO:0000112 "an epidemic" xsd:string -property_value: IAO:0000112 "the undetached arm of a human being" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string -property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000141 -name: immaterial entity -is_a: BFO:0000004 ! independent continuant -property_value: BFO:0000179 "immaterial" xsd:string -property_value: BFO:0000180 "ImmaterialEntity" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: CARO:0000000 @@ -287,29 +164,6 @@ comment: Following BFO, material anatomical entities may have immaterial parts ( is_a: CARO:0030000 ! biological entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl -[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: has_characteristic PATO:0002266 ! 3-D shape -intersection_of: has_characteristic PATO:0010000 ! maximally connected -disjoint_from: CARO:0000004 ! organism substance -relationship: has_characteristic PATO:0002266 ! 3-D shape -relationship: has_characteristic PATO:0010000 ! maximally connected - -[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 @@ -317,161 +171,8 @@ def: "An anatomical entity that has mass." [] subset: core is_a: BFO:0000040 ! material entity is_a: CARO:0000000 ! anatomical entity -intersection_of: CARO:0000000 ! anatomical entity -intersection_of: has_characteristic PATO:0000125 ! mass -disjoint_from: CARO:0000007 ! immaterial anatomical entity -relationship: has_characteristic PATO:0000125 ! mass property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl -[Term] -id: CARO:0000007 -name: immaterial anatomical entity -def: "Anatomical entity that has no mass." [] -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 -is_a: NCBITaxon:131567 ! cellular organisms - -[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: CL:0000003 ! native cell -equivalent_to: CL:0000003 ! native cell -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: part_of CARO:0000013 ! 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: part_of CARO:0000012 ! multicellular organism -property_value: http://purl.obolibrary.org/obo/IAO_creation_date "10.7.2011" xsd:string -property_value: IAO:0000117 "mah" xsd:string - -[Term] -id: CARO:0001010 -name: organism or virus or viroid -def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] -is_a: BFO:0000040 ! material entity -union_of: NCBITaxon:10239 ! Viruses -union_of: NCBITaxon:12884 ! Viroids -union_of: NCBITaxon:131567 ! cellular organisms -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: has_characteristic 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"} ! multicellular -relationship: has_characteristic PATO:0001993 ! multicellular -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: NCBITaxon:131567 ! cellular organisms -equivalent_to: NCBITaxon:131567 ! cellular organisms -property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string -property_value: IAO:0000117 "mah" xsd:string - -[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: has_characteristic PATO:0010001 ! disconnected -intersection_of: RO:0002180 CARO:0000003 {minCardinality="2"} ! has component connected anatomical structure -relationship: has_characteristic PATO:0010001 ! disconnected -relationship: RO:0002180 CARO:0000003 ! has component connected anatomical structure - [Term] id: CARO:0020003 name: cellular anatomical structure @@ -492,15 +193,6 @@ 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: has_part CARO:0000013 ! cell - -[Term] -id: CL:0000003 -name: native cell -def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [] -comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). -is_a: CARO:0000013 ! cell -property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [Term] id: FBbt:00007001 @@ -602,111 +294,15 @@ id: GO:0016772 name: transferase activity, transferring phosphorus-containing groups is_a: GO:0016740 ! transferase activity -[Term] -id: NCBITaxon:10239 -name: Viruses -is_a: CARO:0001010 ! organism or virus or viroid -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - -[Term] -id: NCBITaxon:12884 -name: Viroids -is_a: CARO:0001010 ! organism or virus or viroid -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - -[Term] -id: NCBITaxon:131567 -name: cellular organisms -is_a: CARO:0010004 ! cellular organism -property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl - [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -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 property_value: IAO:0000589 "quality (PATO)" xsd:string -[Term] -id: PATO:0000051 -name: morphology -namespace: quality -def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [PATOC:GVG] -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0000052 -name: shape -is_a: PATO:0000051 ! morphology - -[Term] -id: PATO:0000125 -name: mass -def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [] -is_a: PATO:0001018 ! physical quality - -[Term] -id: PATO:0000141 -name: structure -namespace: quality -def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [PATOC:GVG] -synonym: "relational structural quality" EXACT [] -is_a: PATO:0000051 ! morphology - -[Term] -id: PATO:0001018 -name: physical quality -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0001241 -name: physical object quality -namespace: quality -def: "A quality which inheres in a continuant." [PATOC:GVG] -synonym: "monadic quality of a continuant" EXACT [] -synonym: "monadic quality of an object" NARROW [] -synonym: "monadic quality of continuant" NARROW [] -synonym: "multiply inhering quality of a physical entity " EXACT [] -synonym: "quality of a continuant" EXACT [] -synonym: "quality of a single physical entity" EXACT [] -synonym: "quality of an object" EXACT [] -synonym: "quality of continuant" EXACT [] -is_a: PATO:0000001 ! quality - -[Term] -id: PATO:0001992 -name: cellularity -is_a: PATO:0001995 ! organismal quality - -[Term] -id: PATO:0001993 -name: multicellular -is_a: PATO:0001992 ! cellularity - -[Term] -id: PATO:0001995 -name: organismal quality -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0002266 -name: 3-D shape -is_a: PATO:0000052 ! shape - -[Term] -id: PATO:0010000 -name: maximally connected -is_a: PATO:0000141 ! structure - -[Term] -id: PATO:0010001 -name: disconnected -is_a: PATO:0000141 ! structure - [Term] id: VFB:10000005 name: cell cluster @@ -753,9 +349,9 @@ 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: 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 @@ -815,10 +411,10 @@ def: "This relation obtains between an objective specification and a planned pro 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 @@ -828,12 +424,12 @@ 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: 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 @@ -844,8 +440,8 @@ 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: 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: 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:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string domain: BFO:0000034 ! function @@ -857,8 +453,8 @@ 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: 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: 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:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string is_a: characteristic_of ! characteristic_of @@ -869,8 +465,8 @@ 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: 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: 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:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string is_a: characteristic_of ! characteristic_of @@ -880,33 +476,33 @@ inverse_of: RO:0000087 ! has role 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: 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: 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:0000118 "has_function" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function -is_a: has_characteristic ! has_characteristic +is_a: has_characteristic ! 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: 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: 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:0000118 "has_quality" xsd:string range: BFO:0000019 ! quality -is_a: has_characteristic ! has_characteristic +is_a: has_characteristic ! 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: 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: 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:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role -is_a: has_characteristic ! has_characteristic +is_a: has_characteristic ! has characteristic [Typedef] id: RO:0000091 @@ -914,7 +510,7 @@ 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: has_characteristic ! has characteristic inverse_of: RO:0000092 ! disposition of [Typedef] @@ -1052,11 +648,9 @@ is_a: BFO:0000063 ! precedes 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." [] -comment: For use in recording has_part with a cardinality constraint. -comment: Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ? 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 @@ -1066,7 +660,7 @@ is_a: has_part ! has part 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: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string +property_value: example_of_usage "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: BFO:0000002 ! continuant @@ -1108,7 +702,7 @@ 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: 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: 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: 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 @@ -1119,7 +713,7 @@ 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: 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: 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: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -1148,7 +742,7 @@ 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: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 @@ -1170,7 +764,7 @@ property_value: RO:0001900 RO:0001901 id: RO:0002327 name: enables subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: example_of_usage "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string property_value: IAO:0000118 "executes" xsd:string @@ -1262,7 +856,7 @@ 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: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: example_of_usage "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 @@ -1311,8 +905,8 @@ inverse_of: RO:0002412 ! immediately causally upstream of id: RO:0002410 name: causally related to def: "This relation groups causal relations between material entities and causal relations between processes" [] +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:0000114 IAO:0000428 -property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -1343,7 +937,7 @@ id: RO:0002418 name: causally upstream of or within def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] synonym: "affects" RELATED [] -property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true @@ -1394,7 +988,7 @@ 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: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -1408,8 +1002,8 @@ 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: 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: 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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI @@ -1432,7 +1026,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: editor_note "Axiomatization to GO to be added later" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string is_a: RO:0002436 ! molecularly interacts with @@ -1513,7 +1107,7 @@ property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: 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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string @@ -1574,7 +1168,7 @@ 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: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: example_of_usage "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: has_part capable_of is_a: RO:0002328 ! functionally related to @@ -1584,7 +1178,7 @@ 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: 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: 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:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations domain: BFO:0000040 ! material entity @@ -1595,7 +1189,7 @@ 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: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: example_of_usage "pyrethroid -> growth" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -1612,7 +1206,7 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: example_of_usage "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 positively_regulates is_a: RO:0002596 ! capable of regulating @@ -1735,7 +1329,7 @@ is_a: RO:0002566 ! causally influences id: RO:0017001 name: utilizes def: "X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y." [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string +property_value: example_of_usage "A diagnostic testing device utilizes a specimen." xsd:string property_value: IAO:0000117 "Asiyah Lin" xsd:string property_value: IAO:0000117 "https://orcid.org/0000-0001-9625-1899 Bill Duncan" xsd:string 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 @@ -1809,8 +1403,8 @@ 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: 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: 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 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 @@ -1842,14 +1436,30 @@ 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: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: has_characteristic ! has_characteristic +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: editor_note +name: editor note +namespace: uberon +xref: IAO:0000116 +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + +[Typedef] +id: example_of_usage +name: example of usage +namespace: uberon +xref: IAO:0000112 +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true [Typedef] id: expresses @@ -1868,10 +1478,10 @@ 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: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 @@ -1890,15 +1500,14 @@ 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: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: IAO:0000412 http://purl.obolibrary.org/obo/BFO property_value: RO:0001900 RO:0001901 is_transitive: true is_a: overlaps ! overlaps @@ -1964,15 +1573,14 @@ 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: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: IAO:0000412 http://purl.obolibrary.org/obo/BFO property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 @@ -2016,8 +1624,8 @@ 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: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "David Hill" xsd:string property_value: IAO:0000117 "Tanya Berardini" xsd:string diff --git a/vfbext.owl b/vfbext.owl index 28376ef..d06fb4d 100644 --- a/vfbext.owl +++ b/vfbext.owl @@ -9,7 +9,6 @@ xmlns:vfb="http://purl.obolibrary.org/obo/fbbt/vfb#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:caro="http://purl.obolibrary.org/obo/caro#" xmlns:fbbt="http://purl.obolibrary.org/obo/fbbt#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" @@ -24,10 +23,10 @@ An ontology of miscellaneous terms for data annotation in VFB. VFB Extension Ontology - https://creativecommons.org/licenses/by/3.0/</terms:license> - 24:01:2022 13:12 + https://creativecommons.org/licenses/by/4.0/</terms:license> + 25:02:2022 15:21 VFB extension ontology - 2022-01-24 + 2022-02-25 @@ -63,7 +62,16 @@ - + + IAO:0000112 + uberon + example_of_usage + true + example_of_usage + + example of usage + example of usage + @@ -86,7 +94,16 @@ - + + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + editor note + @@ -134,7 +151,10 @@ - + + + elucidation + @@ -156,12 +176,6 @@ - - - - - - @@ -250,22 +264,6 @@ - - - - - - - - - - - - - - - - @@ -510,15 +508,11 @@ - - - - - - - + + has_obo_namespace + @@ -542,6 +536,12 @@ + + + + + + @@ -554,6 +554,12 @@ + + + + + + @@ -600,7 +606,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of - @@ -645,7 +650,6 @@ 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 @@ -1237,7 +1241,6 @@ Examples include: the relationship between two channels collected simultaneously - @@ -1290,8 +1293,6 @@ Examples include: the relationship between two channels collected simultaneously 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. - For use in recording has_part with a cardinality constraint. - Use: http://purl.obolibrary.org/obo/BFO_0000073 'has cardinal part' ? has component @@ -2704,6 +2705,7 @@ For example, A and B may be gene products and binding of B by A positively regul + entity Entity Julius Caesar @@ -2932,44 +2934,8 @@ For example, A and B may be gene products and binding of B by A positively regul - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - disposition - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - @@ -2984,45 +2950,9 @@ For example, A and B may be gene products and binding of B by A positively regul - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet 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. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - realizable entity - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - @@ -3036,45 +2966,8 @@ For example, A and B may be gene products and binding of B by A positively regul - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - quality - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - @@ -3089,59 +2982,9 @@ For example, A and B may be gene products and binding of B by A positively regul - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - specifically dependent continuant - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - @@ -3149,34 +2992,9 @@ For example, A and B may be gene products and binding of B by A positively regul - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role 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. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - role - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - @@ -3190,29 +3008,9 @@ For example, A and B may be gene products and binding of B by A positively regul - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - generically dependent continuant - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - @@ -3220,29 +3018,8 @@ For example, A and B may be gene products and binding of B by A positively regul - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - function - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - @@ -3250,83 +3027,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - material entity - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - @@ -3334,10 +3037,6 @@ 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 @@ -3354,89 +3053,11 @@ 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anatomical entity that has mass. CARO:0000006 @@ -3447,387 +3068,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - - - - - - Anatomical entity that has no mass. - CARO:0000007 - - immaterial anatomical entity - - - - - - - - - - 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 - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 - - - - - - - - - - - - - - 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 - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - 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 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. - mah - 10.7.2011 - - gross anatomical part - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - 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 - - - - - - - - - - An individual member of a clade of cellular organisms. - mah - 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 - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. - CARO:0000054 - - disconnected anatomical group - - - - - - - - - - - - - - - An anatomical structure consisting of one or more cells. 2018-09-28T14:20:19Z cellular anatomical structure dos - - - - - - - - - - - - - - - With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell - @@ -3846,30 +3095,12 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - The mereological sum of all cells in a single organism in which expression of some specified gene occurs. expression pattern - - - - - A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - - To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). - native cell - - - - @@ -3887,7 +3118,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process 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 + CARO:MAH FBC:DOS @@ -3966,7 +3197,7 @@ MH: sexual subtypes should probably be logically defined based on sexual process Anatomical entity which is part_of Drosophila melanogaster. - CARO:MAH + CARO:MAH @@ -4060,36 +3291,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - Viruses - - - - - - - - - - Viroids - - - - - - - - - - cellular organisms - - - - @@ -4101,10 +3302,8 @@ MH: sexual subtypes should probably be logically defined based on sexual process 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. quality (PATO) PATO:0000072 - trait quality PATO:0000001 quality @@ -4115,158 +3314,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process 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 quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - quality - PATO:0000051 - morphology - - - - - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - PATOC:GVG - - - - - - - - - shape - - - - - - - - - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - PATO:0000125 - mass - - - - - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - relational structural quality - quality - PATO:0000141 - structure - - - - - A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. - PATOC:GVG - - - - - - - - - physical quality - - - - - - - - - A quality which inheres in a continuant. - monadic quality of a continuant - multiply inhering quality of a physical entity - quality of a continuant - quality of a single physical entity - quality of an object - quality of continuant - monadic quality of an object - monadic quality of continuant - quality - PATO:0001241 - physical object quality - - - - - A quality which inheres in a continuant. - PATOC:GVG - - - - - - - - - cellularity - - - - - - - - - multicellular - - - - - - - - - organismal quality - - - - - - - - - 3-D shape - - - - - - - - - maximally connected - - - - - - - - - disconnected - @@ -4363,33 +3410,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - Should belong in BFO, but lives in caro for now. - @@ -4423,22 +3443,6 @@ MH: sexual subtypes should probably be logically defined based on sexual process - - - - - - - - - - - - - - - -