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ro_import.obo
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format-version: 1.2
ontology: envo/imports/ro_import
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/BFO_0000004>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/BFO_0000006>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/PATO_0001199>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/RO_0002577>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000050>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000055>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000066>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000052>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000053>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000056>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000057>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0001025>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002008>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002170>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002176>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002215>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002234>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002379>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002418>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002566>))\nDeclaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0003000>))\n############################\n# Object Properties\n############################\n\n# Object Property: <http://purl.obolibrary.org/obo/RO_0001025> (<http://purl.obolibrary.org/obo/RO_0001025>)\n\nObjectPropertyRange(<http://purl.obolibrary.org/obo/RO_0001025> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000004> ObjectComplementOf(<http://purl.obolibrary.org/obo/BFO_0000006>)))\n\n# Object Property: <http://purl.obolibrary.org/obo/RO_0002008> (<http://purl.obolibrary.org/obo/RO_0002008>)\n\nObjectPropertyRange(<http://purl.obolibrary.org/obo/RO_0002008> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/PATO_0001199>)))\n\n# Object Property: <http://purl.obolibrary.org/obo/RO_0002170> (<http://purl.obolibrary.org/obo/RO_0002170>)\n\nObjectPropertyRange(<http://purl.obolibrary.org/obo/RO_0002170> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/RO_0002577>))\n\n# Object Property: <http://purl.obolibrary.org/obo/RO_0002176> (<http://purl.obolibrary.org/obo/RO_0002176>)\n\nObjectPropertyRange(<http://purl.obolibrary.org/obo/RO_0002176> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/RO_0002577>))\n\n\n############################\n# Classes\n############################\n\n# Class: <http://purl.obolibrary.org/obo/BFO_0000002> (<http://purl.obolibrary.org/obo/BFO_0000002>)\n\nDisjointClasses(<http://purl.obolibrary.org/obo/BFO_0000002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000003>))\n\n# Class: <http://purl.obolibrary.org/obo/BFO_0000003> (<http://purl.obolibrary.org/obo/BFO_0000003>)\n\nDisjointClasses(<http://purl.obolibrary.org/obo/BFO_0000003> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/BFO_0000002>))\n\n\nSubClassOf(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002566> <http://purl.obolibrary.org/obo/BFO_0000040>) ObjectUnionOf(ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000056> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002418> <http://purl.obolibrary.org/obo/BFO_0000015>)) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002215> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000056> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002418> <http://purl.obolibrary.org/obo/BFO_0000015>)))))\nSubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/BFO_0000055> <http://purl.obolibrary.org/obo/RO_0000052>) <http://purl.obolibrary.org/obo/RO_0000057>)\nSubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/RO_0001025> ObjectInverseOf(<http://purl.obolibrary.org/obo/RO_0001025>)) <http://purl.obolibrary.org/obo/RO_0002379>)\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(<http://purl.obolibrary.org/obo/BFO_0000066>) <http://purl.obolibrary.org/obo/RO_0002234>) <http://purl.obolibrary.org/obo/RO_0003000>)\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(<http://purl.obolibrary.org/obo/RO_0002176>) <http://purl.obolibrary.org/obo/RO_0002176>) <http://purl.obolibrary.org/obo/RO_0002170>)\n)
[Term]
id: RO:0002577
name: system
def: "A material entity consisting of multiple components that are causally integrated." []
is_a: BFO:0000040
property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string
[Typedef]
id: BFO:0000050
name: part of
def: "a core relation that holds between a part and its whole" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "is part of" xsd:string
property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string
property_value: IAO:0000118 "part_of" xsd:string
property_value: RO:0001900 RO:0001901
property_value: RO:0040042 BFO:0000002
property_value: RO:0040042 BFO:0000003
property_value: RO:0040042 BFO:0000004
property_value: RO:0040042 BFO:0000017
property_value: RO:0040042 BFO:0000019
property_value: RO:0040042 BFO:0000020
property_value: RO:0040042 BFO:0000031
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
property_value: seeAlso https://wiki.geneontology.org/Part_of xsd:anyURI
is_transitive: true
is_a: RO:0002131 ! overlaps
inverse_of: BFO:0000051 ! has part
[Typedef]
id: BFO:0000051
name: has part
def: "a core relation that holds between a whole and its part" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "has part" xsd:string
property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string
property_value: IAO:0000118 "has_part" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true
is_a: RO:0002131 ! overlaps
[Typedef]
id: BFO:0000054
name: realized in
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
property_value: IAO:0000111 "realized in" xsd:string
property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string
property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string
property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string
property_value: IAO:0000118 "is realized by" xsd:string
property_value: IAO:0000118 "realized_in" xsd:string
property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
domain: BFO:0000017
range: BFO:0000015
inverse_of: BFO:0000055 ! realizes
[Typedef]
id: BFO:0000055
name: realizes
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
property_value: IAO:0000111 "realizes" xsd:string
property_value: IAO:0000112 "this disease course realizes this disease" xsd:string
property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string
property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string
property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
domain: BFO:0000015
range: BFO:0000017
[Typedef]
id: BFO:0000062
name: preceded by
def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: http://purl.org/dc/terms/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string
property_value: IAO:0000111 "preceded by" xsd:string
property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string
property_value: IAO:0000118 "is preceded by" xsd:string
property_value: IAO:0000118 "preceded_by" xsd:string
domain: BFO:0000003
range: BFO:0000003
holds_over_chain: BFO:0000050 BFO:0000062
holds_over_chain: RO:0002091 BFO:0000062
holds_over_chain: RO:0002092 BFO:0000062
is_transitive: true
is_a: RO:0002086 ! ends after
inverse_of: BFO:0000063 ! precedes
[Typedef]
id: BFO:0000063
name: precedes
def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: IAO:0000111 "precedes" xsd:string
domain: BFO:0000003
range: BFO:0000003
holds_over_chain: BFO:0000050 BFO:0000063
holds_over_chain: RO:0002092 BFO:0000063
is_transitive: true
is_a: RO:0002222 ! temporally related to
[Typedef]
id: BFO:0000066
name: occurs in
def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000111 "occurs in" xsd:string
property_value: IAO:0000118 "occurs_in" xsd:string
property_value: IAO:0000118 "unfolds in" xsd:string
property_value: IAO:0000118 "unfolds_in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
property_value: seeAlso https://wiki.geneontology.org/Occurs_in xsd:anyURI
domain: BFO:0000003
range: BFO:0000004
holds_over_chain: BFO:0000050 BFO:0000066
inverse_of: BFO:0000067 ! contains process
transitive_over: BFO:0000050 ! part of
[Typedef]
id: BFO:0000067
name: contains process
def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
property_value: IAO:0000111 "site of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
[Typedef]
id: RO:0000052
name: characteristic of
def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." []
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
property_value: IAO:0000111 "inheres in" xsd:string
property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string
property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string
property_value: IAO:0000118 "inheres_in" xsd:string
property_value: RO:0001900 RO:0001901
is_functional: true
is_a: RO:0002314 ! characteristic of part of
inverse_of: RO:0000053 ! has characteristic
[Typedef]
id: RO:0000053
name: has characteristic
def: "Inverse of characteristic_of" []
property_value: IAO:0000111 "bearer of" xsd:string
property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string
property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
range: BFO:0000020
is_inverse_functional: true
[Typedef]
id: RO:0000056
name: participates in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
property_value: 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
range: BFO:0000003
inverse_of: RO:0000057 ! has participant
[Typedef]
id: RO:0000057
name: has participant
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
property_value: http://purl.org/dc/terms/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string
property_value: IAO:0000111 "has participant" xsd:string
property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string
property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string
property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string
property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string
property_value: IAO:0000118 "has_participant" xsd:string
domain: BFO:0000003
range: BFO:0000002
holds_over_chain: BFO:0000051 RO:0000057
[Typedef]
id: RO:0000058
name: is concretized as
def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." []
property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string
property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string
domain: BFO:0000031
range: BFO:0000020
inverse_of: RO:0000059 ! concretizes
[Typedef]
id: RO:0000059
name: concretizes
def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." []
property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string
property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string
domain: BFO:0000020
range: BFO:0000031
[Typedef]
id: RO:0000079
name: function of
def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string
property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string
property_value: IAO:0000118 "function_of" xsd:string
property_value: IAO:0000118 "is function of" xsd:string
domain: BFO:0000034
is_a: RO:0000052 ! characteristic of
inverse_of: RO:0000085 ! has function
[Typedef]
id: RO:0000080
name: quality of
def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" []
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: IAO:0000118 "is quality of" xsd:string
property_value: IAO:0000118 "quality_of" xsd:string
is_a: RO:0000052 ! characteristic of
inverse_of: RO:0000086 ! has quality
[Typedef]
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: IAO:0000118 "is role of" xsd:string
property_value: IAO:0000118 "role_of" xsd:string
is_a: RO:0000052 ! characteristic of
inverse_of: RO:0000087 ! has role
[Typedef]
id: RO:0000085
name: has function
def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string
property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string
property_value: IAO:0000118 "has_function" xsd:string
domain: BFO:0000004
range: BFO:0000034
is_a: RO:0000053 ! has characteristic
[Typedef]
id: RO:0000086
name: has quality
def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this apple has quality this red color" xsd:string
property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "has_quality" xsd:string
range: BFO:0000019
is_a: RO:0000053 ! has characteristic
[Typedef]
id: RO:0000087
name: has role
def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string
property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string
property_value: IAO:0000118 "has_role" xsd:string
domain: BFO:0000004
range: BFO:0000023
is_a: RO:0000053 ! has characteristic
[Typedef]
id: RO:0000091
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
range: BFO:0000016
is_a: RO:0000053 ! has characteristic
inverse_of: RO:0000092 ! disposition of
[Typedef]
id: RO:0000092
name: disposition of
def: "inverse of has disposition" []
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
subset: RO:0002259
is_a: RO:0000052 ! characteristic of
[Typedef]
id: RO:0001000
name: derives from
def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" []
subset: ro-eco
property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string
property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string
property_value: IAO:0000118 "derives_from" xsd:string
property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string
inverse_of: RO:0001001 ! derives into
[Typedef]
id: RO:0001001
name: derives into
def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" []
subset: ro-eco
property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string
property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string
property_value: IAO:0000118 "derives_into" xsd:string
[Typedef]
id: RO:0001015
name: location of
def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" []
property_value: IAO:0000111 "is location of" xsd:string
property_value: IAO:0000112 "my head is the location of my brain" xsd:string
property_value: IAO:0000112 "this cage is the location of this rat" xsd:string
property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000118 "location_of" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true
inverse_of: RO:0001025 ! located in
[Typedef]
id: RO:0001018
name: obsolete contained in
property_value: IAO:0000111 "contained in" xsd:string
property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string
property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string
property_value: IAO:0000118 "contained_in" xsd:string
property_value: seeAlso https://github.com/oborel/obo-relations/issues/693
is_obsolete: true
[Typedef]
id: RO:0001019
name: obsolete contains
property_value: IAO:0000111 "contains" xsd:string
property_value: seeAlso https://github.com/oborel/obo-relations/issues/693
is_obsolete: true
[Typedef]
id: RO:0001025
name: located in
def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" []
subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
property_value: http://purl.org/dc/terms/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string
property_value: IAO:0000111 "located in" xsd:string
property_value: IAO:0000112 "my brain is located in my head" xsd:string
property_value: IAO:0000112 "this rat is located in this cage" xsd:string
property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string
property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000118 "located_in" xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso https://wiki.geneontology.org/Located_in xsd:anyURI
domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."}
range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."}
is_transitive: true
transitive_over: BFO:0000050 ! part of
[Typedef]
id: RO:0002007
name: bounding layer of
def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" []
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
subset: ro-eco
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
range: BFO:0000040
is_a: BFO:0000050 ! part of
[Typedef]
id: RO:0002008
name: coincident with
def: "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." []
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
subset: ro-eco
property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
is_a: RO:0002323 ! mereotopologically related to
[Typedef]
id: RO:0002084
name: during which ends
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_a: RO:0002222 ! temporally related to
inverse_of: RO:0002093 ! ends during
[Typedef]
id: RO:0002085
name: encompasses
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
property_value: IAO:0000118 "di" xsd:string
is_transitive: true
is_a: RO:0002088 ! during which starts
inverse_of: RO:0002092 ! happens during
[Typedef]
id: RO:0002086
name: ends after
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
holds_over_chain: RO:0002093 BFO:0000062
is_transitive: true
is_a: RO:0002222 ! temporally related to
[Typedef]
id: RO:0002087
name: immediately preceded by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "starts_at_end_of" xsd:string
holds_over_chain: RO:0002224 RO:0002230
is_a: BFO:0000062 ! preceded by
inverse_of: RO:0002090 ! immediately precedes
[Typedef]
id: RO:0002088
name: during which starts
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_a: RO:0002222 ! temporally related to
inverse_of: RO:0002091 ! starts during
[Typedef]
id: RO:0002090
name: immediately precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
property_value: IAO:0000118 "ends_at_start_of" xsd:string
property_value: IAO:0000118 "meets" xsd:string
property_value: RO:0002575 BFO:0000063
holds_over_chain: RO:0002230 RO:0002224
is_a: BFO:0000063 ! precedes
[Typedef]
id: RO:0002091
name: starts during
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "io" xsd:string
domain: BFO:0000003
range: BFO:0000003
is_a: RO:0002222 ! temporally related to
[Typedef]
id: RO:0002092
name: happens during
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
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
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "d" xsd:string
property_value: IAO:0000118 "during" xsd:string
property_value: seeAlso https://wiki.geneontology.org/Happens_during xsd:anyURI
is_transitive: true
is_a: RO:0002091 ! starts during
is_a: RO:0002093 ! ends during
[Typedef]
id: RO:0002093
name: ends during
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "o" xsd:string
property_value: IAO:0000118 "overlaps" xsd:string
is_a: RO:0002222 ! temporally related to
[Typedef]
id: RO:0002131
name: overlaps
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_gocam
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: RO:0001900 RO:0001901
holds_over_chain: BFO:0000050 BFO:0000050
holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
holds_over_chain: BFO:0000051 RO:0002131
is_symmetric: true
is_a: RO:0002323 ! mereotopologically related to
transitive_over: BFO:0000050 ! part of
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []
[Typedef]
id: RO:0002150
name: continuous with
def: "X continuous_with Y if and only if X and Y share a fiat boundary." []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
property_value: IAO:0000118 "connected to" xsd:string
property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso FMA:85972 xsd:string
domain: BFO:0000004
range: BFO:0000004
is_symmetric: true
is_a: RO:0002323 ! mereotopologically related to
[Typedef]
id: RO:0002151
name: partially overlaps
def: "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" xsd:string
property_value: IAO:0000118 "proper overlaps" xsd:string
property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (proper_overlaps ?x ?y)\n (and \n (overlaps ?x ?y)\n (not (part_of ?x ?y)) \n (not (part_of ?y ?x)))))" xsd:string
property_value: RO:0001900 RO:0001901
is_a: RO:0002131 ! overlaps
[Typedef]
id: RO:0002162
name: in taxon
def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." []
comment: Connects a biological entity to its taxon of origin.
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints
range: OBI:0100026
holds_over_chain: BFO:0000050 RO:0002162
holds_over_chain: BFO:0000051 RO:0002162
holds_over_chain: RO:0002202 RO:0002162
holds_over_chain: RO:0002215 RO:0002162
holds_over_chain: RO:0002225 RO:0002162
holds_over_chain: RO:0002254 RO:0002162
holds_over_chain: RO:0002295 RO:0002162
is_a: RO:0002320 ! evolutionarily related to
[Typedef]
id: RO:0002163
name: spatially disjoint from
def: "A is spatially_disjoint_from B if and only if they have no parts in common" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI
is_a: RO:0002323 ! mereotopologically related to
expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" []
[Typedef]
id: RO:0002170
name: connected to
def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" []
property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI
is_a: RO:0002323 ! mereotopologically related to
[Typedef]
id: RO:0002176
name: connects
def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." []
property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string
property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI
domain: BFO:0000004
is_a: RO:0002323 ! mereotopologically related to
[Typedef]
id: RO:0002177
name: attached to part of
def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." []
property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string
domain: UBERON:0000061
range: UBERON:0000061
holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002323 ! mereotopologically related to
is_a: RO:0002567 ! biomechanically related to
[Typedef]
id: RO:0002179
name: drains
def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." []
property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
is_a: RO:0002170 ! connected to
[Typedef]
id: RO:0002180
name: has component
def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string
property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency
is_a: BFO:0000051 ! has part
[Typedef]
id: RO:0002202
name: develops from
def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" []
comment: This is the transitive form of the develops from relation
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228
domain: BFO:0000004
range: BFO:0000004
is_transitive: true
is_a: RO:0002254 ! has developmental contribution from
is_a: RO:0002258 ! developmentally preceded by
inverse_of: RO:0002203 ! develops into
[Typedef]
id: RO:0002203
name: develops into
def: "inverse of develops from" []
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228
is_transitive: true
is_a: RO:0002286 ! developmentally succeeded by
is_a: RO:0002387 ! has potential to develop into
is_a: RO:0002388 ! has potential to directly develop into
[Typedef]
id: RO:0002207
name: directly develops from
def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." []
comment: TODO - add child relations from DOS
synonym: "has developmental precursor" EXACT []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172
property_value: IAO:0000119 "FBbt" xsd:string
property_value: RO:0002575 RO:0002202
is_a: RO:0002202 ! develops from
inverse_of: RO:0002210 ! directly develops into
[Typedef]
id: RO:0002210
name: directly develops into
def: "inverse of directly develops from" []
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000118 "developmental precursor of" xsd:string
is_a: RO:0002203 ! develops into
[Typedef]
id: RO:0002211
name: regulates
def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306
property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 "GO" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string
property_value: IAO:0000589 "regulates (processual)" xsd:string
property_value: IAO:0000600 "false" xsd:boolean
domain: BFO:0000015
range: BFO:0000015
holds_over_chain: RO:0002230 RO:0002211
is_transitive: true
is_a: RO:0002411 ! causally upstream of
inverse_of: RO:0002334 ! regulated by
[Typedef]
id: RO:0002212
name: negatively regulates
def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
property_value: RO:0004050 RO:0002211
holds_over_chain: RO:0002230 RO:0002212
is_a: RO:0002211 ! regulates
is_a: RO:0002305 ! causally upstream of, negative effect
inverse_of: RO:0002335 ! negatively regulated by
[Typedef]
id: RO:0002213
name: positively regulates
def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
property_value: RO:0004049 RO:0002211
holds_over_chain: RO:0002212 RO:0002212
holds_over_chain: RO:0002230 RO:0002213
is_transitive: true
is_a: RO:0002211 ! regulates
is_a: RO:0002304 ! causally upstream of, positive effect
inverse_of: RO:0002336 ! positively regulated by
[Typedef]
id: RO:0002215
name: capable of
def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " []
subset: ro-eco
property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "has function realized in" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450
property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string
domain: BFO:0000004
range: BFO:0000015
is_a: RO:0002216 ! capable of part of
[Typedef]
id: RO:0002216
name: capable of part of
def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "has function in" xsd:string
property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/
holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process
[Typedef]
id: RO:0002217
name: obsolete actively participates in
def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" []
comment: Obsoleted as the inverse property was obsoleted.
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "agent in" xsd:string
is_obsolete: true
replaced_by: RO:0002608
[Typedef]
id: RO:0002218
name: obsolete has active participant
def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" []
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "has agent" xsd:string
is_obsolete: true
replaced_by: RO:0002500
[Typedef]
id: RO:0002219
name: surrounded by
def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: RO:0001900 RO:0001901
is_a: RO:0002220 ! adjacent to
inverse_of: RO:0002221 ! surrounds
[Typedef]
id: RO:0002220
name: adjacent to
def: "x adjacent to y if and only if x and y share a boundary." []
subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension
subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
subset: http://purl.obolibrary.org/obo/valid_for_gocam
property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"}
property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string
property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string
property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: RO:0001900 RO:0001901
domain: BFO:0000004
range: BFO:0000004
is_a: RO:0002163 ! spatially disjoint from
[Typedef]
id: RO:0002221
name: surrounds
def: "inverse of surrounded by" []
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: RO:0001900 RO:0001901
is_a: RO:0002220 ! adjacent to
[Typedef]
id: RO:0002222
name: temporally related to
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
subset: ro-eco
property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra
property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string
domain: BFO:0000003
range: BFO:0000003
[Typedef]
id: RO:0002223
name: starts
def: "inverse of starts with" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 "Allen" xsd:string
is_a: BFO:0000050 ! part of
is_a: RO:0002222 ! temporally related to
inverse_of: RO:0002224 ! starts with
[Typedef]
id: RO:0002224
name: starts with
def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "started by" xsd:string
is_transitive: true
is_a: BFO:0000051 ! has part
is_a: RO:0002222 ! temporally related to
[Typedef]
id: RO:0002225
name: develops from part of
def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
holds_over_chain: RO:0002207 BFO:0000050
is_a: RO:0002202 ! develops from
[Typedef]
id: RO:0002226
name: develops in
def: "x develops_in y if x is located in y whilst x is developing" []
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000119 "EHDAA2" xsd:string
property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string
domain: UBERON:0001062
holds_over_chain: RO:0002207 RO:0001025
is_a: RO:0002258 ! developmentally preceded by
[Typedef]
id: RO:0002229
name: ends
def: "inverse of ends with" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
is_a: BFO:0000050 ! part of
is_a: RO:0002222 ! temporally related to
inverse_of: RO:0002230 ! ends with
[Typedef]
id: RO:0002230
name: ends with
def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "finished by" xsd:string
is_transitive: true
is_a: BFO:0000051 ! has part
is_a: RO:0002222 ! temporally related to
[Typedef]
id: RO:0002231
name: has start location
def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "starts with process that occurs in" xsd:string
domain: BFO:0000015
range: BFO:0000004
holds_over_chain: RO:0002224 BFO:0000066
is_a: RO:0002479 ! has part that occurs in
[Typedef]
id: RO:0002232
name: has end location
def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" []
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "ends with process that occurs in" xsd:string
domain: BFO:0000015
range: BFO:0000004
holds_over_chain: RO:0002230 BFO:0000066
is_a: RO:0002479 ! has part that occurs in
[Typedef]
id: RO:0002233
name: has input
def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." []
subset: 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
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "consumes" xsd:string
property_value: seeAlso https://wiki.geneontology.org/Has_input xsd:anyURI
domain: BFO:0000015
holds_over_chain: RO:0002224 RO:0002233
is_a: RO:0000057 ! has participant
inverse_of: RO:0002352 ! input of
[Typedef]
id: RO:0002234
name: has output
def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." []
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
subset: ro-eco
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "produces" xsd:string
property_value: seeAlso https://wiki.geneontology.org/Has_output xsd:anyURI
holds_over_chain: RO:0002230 RO:0002234
is_a: RO:0000057 ! has participant
inverse_of: RO:0002353 ! output of
[Typedef]
id: RO:0002254
name: has developmental contribution from
def: "x has developmental contribution from y iff x has some part z such that z develops from y" []
property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
domain: UBERON:0001062
range: UBERON:0001062
holds_over_chain: BFO:0000051 RO:0002202
is_a: RO:0002258 ! developmentally preceded by
inverse_of: RO:0002255 ! developmentally contributes to
[Typedef]
id: RO:0002255
name: developmentally contributes to
def: "inverse of has developmental contribution from" []
subset: RO:0002259
property_value: IAO:0000114 IAO:0000125
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
holds_over_chain: RO:0002203 BFO:0000050