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ro.yaml
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ro.yaml
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---
graphs:
- id: "http://purl.obolibrary.org/obo/ro.owl"
meta:
basicPropertyValues:
- pred: "http://purl.org/dc/elements/1.1/description"
val: "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties)\
\ intended for use across a wide variety of biological ontologies."
- pred: "http://purl.org/dc/elements/1.1/source"
val: "http://obofoundry.org/ro"
- pred: "http://purl.org/dc/elements/1.1/title"
val: "OBO Relations Ontology"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms:\
\ 0]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms:\
\ 0]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/annotations.owl>)\
\ VersionIRI(<null>))) [Axioms: 61 Logical Axioms: 0]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-classes-minimal.owl>)\
\ VersionIRI(<null>))) [Axioms: 53 Logical Axioms: 12]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/core.owl>)\
\ VersionIRI(<null>))) [Axioms: 276 Logical Axioms: 56]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/el-constraints.owl>)\
\ VersionIRI(<null>))) [Axioms: 6 Logical Axioms: 2]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/go-biotic.owl>)\
\ VersionIRI(<null>))) [Axioms: 42 Logical Axioms: 16]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/go_mf_import.owl>)\
\ VersionIRI(<null>))) [Axioms: 29 Logical Axioms: 9]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/pato_import.owl>)\
\ VersionIRI(<null>))) [Axioms: 20 Logical Axioms: 6]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/rohom.owl>)\
\ VersionIRI(<null>))) [Axioms: 731 Logical Axioms: 148]"
- pred: "http://www.w3.org/2000/01/rdf-schema#comment"
val: "Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>)\
\ VersionIRI(<null>))) [Axioms: 146 Logical Axioms: 45]"
- pred: "http://xmlns.com/foaf/0.1/homepage"
val: " https://github.com/oborel/obo-relations/"
version: "http://purl.obolibrary.org/obo/ro/releases/2016-09-02/ro.owl"
nodes:
- id: "http://purl.obolibrary.org/obo/BFO_0000002"
lbl: "continuant"
type: "CLASS"
meta:
definition:
val: "An entity that exists in full at any time in which it exists at all,\
\ persists through time while maintaining its identity and has no temporal\
\ parts."
- id: "http://purl.obolibrary.org/obo/BFO_0000003"
lbl: "occurrent"
type: "CLASS"
meta:
definition:
val: "An entity that has temporal parts and that happens, unfolds or develops\
\ through time."
- id: "http://purl.obolibrary.org/obo/BFO_0000004"
lbl: "independent continuant"
type: "CLASS"
meta:
definition:
val: "A continuant that is a bearer of quality and realizable entity entities,\
\ in which other entities inhere and which itself cannot inhere in anything."
- id: "http://purl.obolibrary.org/obo/BFO_0000005"
lbl: "obsolete dependent continuant"
type: "CLASS"
meta:
definition:
val: "A continuant that is either dependent on one or other independent continuant\
\ bearers or inheres in or is borne by other entities."
deprecated: true
- id: "http://purl.obolibrary.org/obo/BFO_0000015"
lbl: "process"
type: "CLASS"
meta:
definition:
val: "An occurrent that has temporal proper parts and for some time t, p s-depends_on\
\ some material entity at t."
- id: "http://purl.obolibrary.org/obo/BFO_0000016"
lbl: "disposition"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/BFO_0000017"
lbl: "realizable entity"
type: "CLASS"
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."
- id: "http://purl.obolibrary.org/obo/BFO_0000019"
lbl: "quality"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/BFO_0000020"
lbl: "specifically dependent continuant"
type: "CLASS"
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."
- id: "http://purl.obolibrary.org/obo/BFO_0000023"
lbl: "role"
type: "CLASS"
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."
- id: "http://purl.obolibrary.org/obo/BFO_0000031"
lbl: "generically dependent continuant"
type: "CLASS"
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."
- id: "http://purl.obolibrary.org/obo/BFO_0000034"
lbl: "function"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/BFO_0000040"
lbl: "material entity"
type: "CLASS"
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."
- id: "http://purl.obolibrary.org/obo/BFO_0000141"
lbl: "immaterial entity"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/CARO_0000003"
lbl: "anatomical structure"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/caro.owl"
- id: "http://purl.obolibrary.org/obo/CARO_0000006"
lbl: "material anatomical entity"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/caro.owl"
- id: "http://purl.obolibrary.org/obo/CARO_0000007"
lbl: "immaterial anatomical entity"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/CARO_0000011"
lbl: "connected anatomical system"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/CARO_0000014"
lbl: "cell part"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/caro.owl"
- pred: "http://purl.obolibrary.org/obo/IAO_0000589"
val: "cell part (CARO)"
- id: "http://purl.obolibrary.org/obo/CARO_0001000"
lbl: "multi-cell-part structure"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/caro.owl"
- id: "http://purl.obolibrary.org/obo/CARO_0001001"
lbl: "neuron projection bundle"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/caro.owl"
- id: "http://purl.obolibrary.org/obo/CARO_0010000"
lbl: "multicellular anatomical structure"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/caro.owl"
- id: "http://purl.obolibrary.org/obo/CL_0000000"
lbl: "cell"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/cl.owl"
- id: "http://purl.obolibrary.org/obo/CL_0000540"
lbl: "neuron"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/cl.owl"
- id: "http://purl.obolibrary.org/obo/ENVO_00000428"
lbl: "biome"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/ENVO_01000254"
lbl: "environmental system"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0003674"
lbl: "molecular_function"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000589"
val: "molecular process"
- id: "http://purl.obolibrary.org/obo/GO_0003824"
lbl: "catalytic activity"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0004842"
lbl: "ubiquitin-protein ligase activity"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0005634"
lbl: "nucleus"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0007610"
lbl: "behavior"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0007631"
lbl: "feeding behavior"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0008150"
lbl: "biological_process"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0016020"
lbl: "membrane"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0016301"
lbl: "kinase activity"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0016740"
lbl: "transferase activity"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0016772"
lbl: "transferase activity, transferring phosphorus-containing groups"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0016874"
lbl: "ligase activity"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0016879"
lbl: "ligase activity, forming carbon-nitrogen bonds"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0016881"
lbl: "acid-amino acid ligase activity"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0019787"
lbl: "small conjugating protein ligase activity"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0030424"
lbl: "axon"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0030425"
lbl: "dendrite"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0040011"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0042734"
lbl: "presynaptic membrane"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0042995"
lbl: "cell projection"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0043005"
lbl: "neuron projection"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0044403"
lbl: "symbiosis, encompassing mutualism through parasitism"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0044419"
lbl: "interspecies interaction between organisms"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0044456"
lbl: "synapse part"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0044464"
lbl: "cell part"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0045202"
lbl: "synapse"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0045211"
lbl: "postsynaptic membrane"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000412"
val: "http://purl.obolibrary.org/obo/go.owl"
- id: "http://purl.obolibrary.org/obo/GO_0050896"
lbl: "response to stimulus"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0051702"
lbl: "interaction with symbiont"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0051704"
lbl: "multi-organism process"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0051705"
lbl: "multi-organism behavior"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0051816"
lbl: "acquisition of nutrients from other organism during symbiotic interaction"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0051850"
lbl: "acquisition of nutrients from symbiont"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0072519"
lbl: "parasitism"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0085030"
lbl: "mutualism"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/GO_0085031"
lbl: "commensalism"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/PATO_0000001"
lbl: "quality"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000589"
val: "quality (PATO)"
- id: "http://purl.obolibrary.org/obo/PATO_0000051"
lbl: "morphology"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/PATO_0000052"
lbl: "shape"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/PATO_0000141"
lbl: "structure"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/PATO_0000402"
lbl: "branched"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/PATO_0001199"
lbl: "linear"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/PATO_0001241"
lbl: "physical object quality"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/PATO_0002009"
lbl: "branchiness"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/PATO_0002124"
lbl: "laminar"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/RO_0002532"
lbl: "sequentially ordered entity"
type: "CLASS"
meta:
definition:
val: "Any entity that is ordered in discrete units along a linear axis."
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000117"
val: "Chris Mungall"
- id: "http://purl.obolibrary.org/obo/RO_0002533"
lbl: "sequence atomic unit"
type: "CLASS"
meta:
definition:
val: "Any individual unit of a collection of like units arranged in a linear\
\ order"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000117"
val: "Chris Mungall"
- pred: "http://purl.obolibrary.org/obo/IAO_0000232"
val: "An individual unit can be a molecular entity such as a base pair, or\
\ an abstract entity, such as the abstraction of a base pair."
- id: "http://purl.obolibrary.org/obo/RO_0002534"
lbl: "sequence bearer"
type: "CLASS"
meta:
definition:
val: "Any entity that can be divided into parts such that each part is an\
\ atomical unit of a sequence"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000117"
val: "Chris Mungall"
- pred: "http://purl.obolibrary.org/obo/IAO_0000232"
val: "Sequence bearers can be molecular entities, such as a portion of a DNA\
\ molecule, or they can be abstract entities, such as an entity representing\
\ all human sonic hedgehog regions of the genome with a particular DNA sequence."
- id: "http://purl.obolibrary.org/obo/RO_0002577"
lbl: "system"
type: "CLASS"
meta:
definition:
val: "A material entity consisting of multiple components that are causally\
\ integrated."
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43"
- pred: "http://purl.obolibrary.org/obo/IAO_0000117"
val: "Chris Mungall"
- pred: "http://purl.obolibrary.org/obo/IAO_0000119"
val: "http://www.jbiomedsem.com/content/4/1/43"
- id: "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"
lbl: "Obsolete Class"
type: "CLASS"
- id: "http://purl.obolibrary.org/obo/BFO_0000050"
lbl: "part of"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a core relation that holds between a part and its whole"
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 https://code.google.com/p/obo-relations/wiki/ROAndTime"
- 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/RO_0001900"
val: "http://purl.obolibrary.org/obo/RO_0001901"
- 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"
- id: "http://purl.obolibrary.org/obo/BFO_0000051"
lbl: "has part"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a core relation that holds between a whole and its part"
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 https://code.google.com/p/obo-relations/wiki/ROAndTime"
- 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/RO_0001900"
val: "http://purl.obolibrary.org/obo/RO_0001901"
- id: "http://purl.obolibrary.org/obo/BFO_0000054"
lbl: "realized in"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
comments:
- "Paraphrase of elucidation: a relation between a realizable entity and a process,\
\ where there is some material entity that is bearer of the realizable entity\
\ and participates in the process, and the realizable entity comes to be realized\
\ in the course of the process"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000111"
val: "realized in"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this disease is realized in this disease course"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this fragility is realized in this shattering"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this investigator role is realized in this investigation"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "is realized by"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "realized_in"
- pred: "http://purl.obolibrary.org/obo/IAO_0000600"
val: "[copied from inverse property 'realizes'] to say that b realizes c at\
\ t is to assert that there is some material entity d & b is a process which\
\ has participant d at t & c is a disposition or role of which d is bearer_of\
\ at t& the type instantiated by b is correlated with the type instantiated\
\ by c. (axiom label in BFO2 Reference: [059-003])"
- pred: "http://www.w3.org/2000/01/rdf-schema#isDefinedBy"
val: "http://purl.obolibrary.org/obo/bfo.owl"
- id: "http://purl.obolibrary.org/obo/BFO_0000055"
lbl: "realizes"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
comments:
- "Paraphrase of elucidation: a relation between a process and a realizable\
\ entity, where there is some material entity that is bearer of the realizable\
\ entity and participates in the process, and the realizable entity comes\
\ to be realized in the course of the process"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000111"
val: "realizes"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this disease course realizes this disease"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this investigation realizes this investigator role"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this shattering realizes this fragility"
- pred: "http://purl.obolibrary.org/obo/IAO_0000600"
val: "to say that b realizes c at t is to assert that there is some material\
\ entity d & b is a process which has participant d at t & c is a disposition\
\ or role of which d is bearer_of at t& the type instantiated by b is correlated\
\ with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"
- pred: "http://www.w3.org/2000/01/rdf-schema#isDefinedBy"
val: "http://purl.obolibrary.org/obo/iao.owl"
- id: "http://purl.obolibrary.org/obo/BFO_0000060"
lbl: "obsolete preceded by"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
comments:
- "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062"
- id: "http://purl.obolibrary.org/obo/BFO_0000062"
lbl: "preceded by"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
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."
subsets:
- "http://purl.obolibrary.org/obo/ro/subsets#ro-eco"
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"
- id: "http://purl.obolibrary.org/obo/BFO_0000063"
lbl: "precedes"
type: "PROPERTY"
propertyType: "ANNOTATION"
meta:
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."
subsets:
- "http://purl.obolibrary.org/obo/ro/subsets#ro-eco"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000111"
val: "precedes"
- id: "http://purl.obolibrary.org/obo/BFO_0000066"
lbl: "occurs in"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "b occurs_in c =def b is a process and c is a material entity or immaterial\
\ entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region\
\ r.& forall(t) if b exists_at t then c exists_at t & there exist spatial\
\ regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region\
\ s’ at t& s is a proper_continuant_part_of s’ at t"
comments:
- "Paraphrase of definition: a relation between a process and an independent\
\ continuant, in which the process takes place entirely within the independent\
\ continuant"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000111"
val: "occurs in"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "occurs_in"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "unfolds in"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "unfolds_in"
- pred: "http://www.w3.org/2000/01/rdf-schema#isDefinedBy"
val: "http://purl.obolibrary.org/obo/bfo.owl"
- id: "http://purl.obolibrary.org/obo/BFO_0000067"
lbl: "contains process"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a\
\ process and c is a material entity or immaterial entity& there exists\
\ a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t)\
\ if b exists_at t then c exists_at t & there exist spatial regions s and\
\ s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region\
\ s’ at t& s is a proper_continuant_part_of s’ at t"
comments:
- "Paraphrase of definition: a relation between an independent continuant and\
\ a process, in which the process takes place entirely within the independent\
\ continuant"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000111"
val: "site of"
- pred: "http://www.w3.org/2000/01/rdf-schema#isDefinedBy"
val: "http://purl.obolibrary.org/obo/bfo.owl"
- id: "http://purl.obolibrary.org/obo/RO_0000052"
lbl: "inheres in"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between a specifically dependent continuant (the dependent)\
\ and an independent continuant (the bearer), in which the dependent specifically\
\ depends on the bearer for its existence"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000111"
val: "inheres in"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this fragility inheres in this vase"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this red color inheres in this apple"
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "A dependent inheres in its bearer at all times for which the dependent\
\ exists."
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "inheres_in"
- pred: "http://purl.obolibrary.org/obo/RO_0001900"
val: "http://purl.obolibrary.org/obo/RO_0001901"
- id: "http://purl.obolibrary.org/obo/RO_0000053"
lbl: "bearer of"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between an independent continuant (the bearer) and a specifically\
\ dependent continuant (the dependent), in which the dependent specifically\
\ depends on the bearer for its existence"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000111"
val: "bearer of"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this apple is bearer of this red color"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this vase is bearer of this fragility"
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "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."
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "bearer_of"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "is bearer of"
- pred: "http://purl.obolibrary.org/obo/RO_0001900"
val: "http://purl.obolibrary.org/obo/RO_0001901"
- id: "http://purl.obolibrary.org/obo/RO_0000056"
lbl: "participates in"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between a continuant and a process, in which the continuant\
\ is somehow involved in the process"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000111"
val: "participates in"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this blood clot participates in this blood coagulation"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this input material (or this output material) participates in this process"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this investigator participates in this investigation"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "participates_in"
- id: "http://purl.obolibrary.org/obo/RO_0000057"
lbl: "has participant"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between a process and a continuant, in which the continuant\
\ is somehow involved in the process"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000111"
val: "has participant"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this blood coagulation has participant this blood clot"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this investigation has participant this investigator"
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this process has participant this input material (or this output material)"
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "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."
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "has_participant"
- pred: "http://purl.org/dc/elements/1.1/source"
val: "http://www.obofoundry.org/ro/#OBO_REL:has_participant"
- id: "http://purl.obolibrary.org/obo/RO_0000058"
lbl: "is concretized as"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "A relationship between a generically dependent continuant and a specifically\
\ dependent continuant, in which the generically dependent continuant depends\
\ on some independent continuant in virtue of the fact that the specifically\
\ dependent continuant also depends on that same independent continuant.\
\ A generically dependent continuant may be concretized as multiple specifically\
\ dependent continuants."
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "A journal article is an information artifact that inheres in some number\
\ of printed journals. For each copy of the printed journal there is some\
\ quality that carries the journal article, such as a pattern of ink. The\
\ journal article (a generically dependent continuant) is concretized as\
\ the quality (a specifically dependent continuant), and both depend on\
\ that copy of the printed journal (an independent continuant)."
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "An investigator reads a protocol and forms a plan to carry out an assay.\
\ The plan is a realizable entity (a specifically dependent continuant)\
\ that concretizes the protocol (a generically dependent continuant), and\
\ both depend on the investigator (an independent continuant). The plan\
\ is then realized by the assay (a process)."
- id: "http://purl.obolibrary.org/obo/RO_0000059"
lbl: "concretizes"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "A relationship between a specifically dependent continuant and a generically\
\ dependent continuant, in which the generically dependent continuant depends\
\ on some independent continuant in virtue of the fact that the specifically\
\ dependent continuant also depends on that same independent continuant.\
\ Multiple specifically dependent continuants can concretize the same generically\
\ dependent continuant."
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "A journal article is an information artifact that inheres in some number\
\ of printed journals. For each copy of the printed journal there is some\
\ quality that carries the journal article, such as a pattern of ink. The\
\ quality (a specifically dependent continuant) concretizes the journal\
\ article (a generically dependent continuant), and both depend on that\
\ copy of the printed journal (an independent continuant)."
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "An investigator reads a protocol and forms a plan to carry out an assay.\
\ The plan is a realizable entity (a specifically dependent continuant)\
\ that concretizes the protocol (a generically dependent continuant), and\
\ both depend on the investigator (an independent continuant). The plan\
\ is then realized by the assay (a process)."
- id: "http://purl.obolibrary.org/obo/RO_0000079"
lbl: "function of"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between a function and an independent continuant (the bearer),\
\ in which the function specifically depends on the bearer for its existence"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this catalysis function is a function of this enzyme"
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "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."
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "function_of"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "is function of"
- id: "http://purl.obolibrary.org/obo/RO_0000080"
lbl: "quality of"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between a quality and an independent continuant (the bearer),\
\ in which the quality specifically depends on the bearer for its existence"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this red color is a quality of this apple"
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "A quality inheres in its bearer at all times for which the quality exists."
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "is quality of"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "quality_of"
- id: "http://purl.obolibrary.org/obo/RO_0000081"
lbl: "role of"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between a role and an independent continuant (the bearer),\
\ in which the role specifically depends on the bearer for its existence"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this investigator role is a role of this person"
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "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."
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "is role of"
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "role_of"
- id: "http://purl.obolibrary.org/obo/RO_0000085"
lbl: "has function"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between an independent continuant (the bearer) and a function,\
\ in which the function specifically depends on the bearer for its existence"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this enzyme has function this catalysis function (more colloquially:\
\ this enzyme has this catalysis function)"
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "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."
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "has_function"
- id: "http://purl.obolibrary.org/obo/RO_0000086"
lbl: "has quality"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between an independent continuant (the bearer) and a quality,\
\ in which the quality specifically depends on the bearer for its existence"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this apple has quality this red color"
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "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."
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "has_quality"
- id: "http://purl.obolibrary.org/obo/RO_0000087"
lbl: "has role"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between an independent continuant (the bearer) and a role,\
\ in which the role specifically depends on the bearer for its existence"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000112"
val: "this person has role this investigator role (more colloquially: this\
\ person has this role of investigator)"
- pred: "http://purl.obolibrary.org/obo/IAO_0000116"
val: "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."
- pred: "http://purl.obolibrary.org/obo/IAO_0000118"
val: "has_role"
- id: "http://purl.obolibrary.org/obo/RO_0000091"
lbl: "has disposition"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "a relation between an independent continuant (the bearer) and a disposition,\
\ in which the disposition specifically depends on the bearer for its existence"
- id: "http://purl.obolibrary.org/obo/RO_0000092"
lbl: "disposition of"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "inverse of has disposition"
subsets:
- "http://purl.obolibrary.org/obo/RO_0002259"
- id: "http://purl.obolibrary.org/obo/RO_0000300"
lbl: "in neural circuit with"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
definition:
val: "A relation that holds between two neurons connected directly via a synapse,\
\ or indirectly via a series of synaptically connected neurons."
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000114"
val: "http://purl.obolibrary.org/obo/IAO_0000125"
- pred: "http://purl.obolibrary.org/obo/IAO_0000117"
val: "David Osumi-Sutherland"
- pred: "http://purl.obolibrary.org/obo/IAO_0000426"