diff --git a/imports/ro_import.obo b/imports/ro_import.obo index fcc4f26a..aa90bac6 100644 --- a/imports/ro_import.obo +++ b/imports/ro_import.obo @@ -1,647 +1,3 @@ format-version: 1.2 -ontology: pato/imports/ro_import -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: ()\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) - -[Term] -id: BFO:0000002 -name: continuant -def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] -disjoint_from: BFO:0000003 ! occurrent - -[Term] -id: BFO:0000003 -name: occurrent -def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] - -[Term] -id: BFO:0000004 -name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] -is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant - -[Term] -id: BFO:0000015 -name: process -def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] -is_a: BFO:0000003 ! occurrent - -[Term] -id: BFO:0000020 -name: specifically dependent continuant -def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -is_a: BFO:0000002 ! continuant - -[Term] -id: BFO:0000040 -name: material entity -def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] -is_a: BFO:0000004 ! independent continuant - -[Term] -id: CARO:0000003 -name: anatomical structure -is_a: CARO:0000006 ! material anatomical entity - -[Term] -id: CARO:0000006 -name: material anatomical entity -is_a: BFO:0000040 ! material entity - -[Term] -id: CARO:0000014 -name: cell part -is_a: CARO:0000003 ! anatomical structure - -[Term] -id: CL:0000000 -name: cell -is_a: CARO:0000003 ! anatomical structure - -[Term] -id: GO:0003674 -name: molecular_function -is_a: BFO:0000015 ! process - -[Term] -id: GO:0004872 -name: receptor activity - -[Term] -id: GO:0005634 -name: nucleus -is_a: GO:0044464 ! cell part -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0008150 -name: biological_process -is_a: BFO:0000015 ! process - -[Term] -id: GO:0044464 -name: cell part -is_a: CARO:0000014 ! cell part -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - -[Typedef] -id: BFO:0000050 -name: part of -def: "a core relation that holds between a part and its whole" [] -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string -is_transitive: true -is_a: RO:0002131 -inverse_of: BFO:0000051 ! has part - -[Typedef] -id: BFO:0000051 -name: has part -def: "a core relation that holds between a whole and its part" [] -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: RO:0002131 - -[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." [] -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000062 -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - -[Typedef] -id: BFO:0000063 -name: precedes -def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -property_value: IAO:0000111 "precedes" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000063 -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: BFO:0000066 -name: occurs in -def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000050 BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: RO:0000052 -name: inheres in -def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string -property_value: IAO:0000112 "this red color inheres in this apple" xsd:string -property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: RO:0002314 -inverse_of: RO:0000053 ! bearer of - -[Typedef] -id: RO:0000053 -name: bearer of -def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant - -[Typedef] -id: RO:0000056 -name: participates in -def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000003 ! occurrent -inverse_of: RO:0000057 ! has participant - -[Typedef] -id: RO:0000057 -name: has participant -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: BFO:0000051 RO:0000057 - -[Typedef] -id: RO:0002013 -is_a: RO:0002017 -is_a: RO:0002334 - -[Typedef] -id: RO:0002014 -is_a: RO:0002013 -is_a: RO:0002335 - -[Typedef] -id: RO:0002015 -is_a: RO:0002013 -is_a: RO:0002336 - -[Typedef] -id: RO:0002017 -is_a: RO:0002018 - -[Typedef] -id: RO:0002018 -is_a: RO:0002180 - -[Typedef] -id: RO:0002019 -domain: GO:0004872 ! receptor activity -is_a: RO:0002233 - -[Typedef] -id: RO:0002022 -is_a: RO:0002334 -inverse_of: RO:0002578 - -[Typedef] -id: RO:0002023 -is_a: RO:0002022 -inverse_of: RO:0002630 - -[Typedef] -id: RO:0002024 -is_a: RO:0002022 -inverse_of: RO:0002629 - -[Typedef] -id: RO:0002025 -is_functional: true -is_a: RO:0002017 -is_a: RO:0002211 - -[Typedef] -id: RO:0002086 -name: ends after -comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -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 -is_a: BFO:0000062 ! preceded by -inverse_of: RO:0002090 ! immediately precedes - -[Typedef] -id: RO:0002090 -name: immediately precedes -comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -is_a: BFO:0000063 ! precedes - -[Typedef] -id: RO:0002131 -holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: BFO:0000051 RO:0002131 -is_a: RO:0002323 - -[Typedef] -id: RO:0002180 -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002211 -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -holds_over_chain: RO:0002578 RO:0002578 -is_transitive: true -is_a: RO:0002411 -inverse_of: RO:0002334 - -[Typedef] -id: RO:0002212 -is_a: RO:0002211 -is_a: RO:0002305 -inverse_of: RO:0002335 - -[Typedef] -id: RO:0002213 -holds_over_chain: RO:0002212 RO:0002212 -is_transitive: true -is_a: RO:0002211 -is_a: RO:0002304 -inverse_of: RO:0002336 - -[Typedef] -id: RO:0002215 -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: RO:0002216 - -[Typedef] -id: RO:0002216 -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002328 -is_a: RO:0002500 - -[Typedef] -id: RO:0002217 -is_a: RO:0000056 ! participates in -inverse_of: RO:0002218 - -[Typedef] -id: RO:0002218 -is_a: RO:0000057 ! has participant - -[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. -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent - -[Typedef] -id: RO:0002233 -domain: BFO:0000015 ! process -range: BFO:0000040 ! material entity -is_a: RO:0000057 ! has participant -inverse_of: RO:0002352 - -[Typedef] -id: RO:0002263 -holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002264 - -[Typedef] -id: RO:0002264 -holds_over_chain: RO:0002327 RO:0002418 -is_a: RO:0002500 - -[Typedef] -id: RO:0002304 -is_a: RO:0002411 -is_a: RO:0004047 - -[Typedef] -id: RO:0002305 -is_a: RO:0002411 -is_a: RO:0004046 - -[Typedef] -id: RO:0002314 -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002502 -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002327 -is_a: RO:0002215 -inverse_of: RO:0002333 -transitive_over: BFO:0000051 ! has part -transitive_over: RO:0002017 - -[Typedef] -id: RO:0002329 -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002328 - -[Typedef] -id: RO:0002331 -holds_over_chain: RO:0002327 BFO:0000050 -is_a: RO:0002217 -is_a: RO:0002431 -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002333 -is_a: RO:0002328 - -[Typedef] -id: RO:0002334 -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_transitive: true -is_a: RO:0002427 - -[Typedef] -id: RO:0002335 -is_a: RO:0002334 - -[Typedef] -id: RO:0002336 -is_a: RO:0002334 - -[Typedef] -id: RO:0002352 -is_a: RO:0000056 ! participates in -is_a: RO:0002328 - -[Typedef] -id: RO:0002404 -is_a: BFO:0000062 ! preceded by -is_a: RO:0002427 -inverse_of: RO:0002411 - -[Typedef] -id: RO:0002405 -is_a: RO:0002087 ! immediately preceded by -is_a: RO:0002404 -inverse_of: RO:0002412 - -[Typedef] -id: RO:0002410 -is_a: RO:0002609 - -[Typedef] -id: RO:0002411 -is_transitive: true -is_a: BFO:0000063 ! precedes -is_a: RO:0002418 - -[Typedef] -id: RO:0002412 -is_a: RO:0002090 ! immediately precedes -is_a: RO:0002411 - -[Typedef] -id: RO:0002418 -is_transitive: true -is_a: RO:0002501 -inverse_of: RO:0002427 - -[Typedef] -id: RO:0002427 -is_transitive: true -is_a: RO:0002501 - -[Typedef] -id: RO:0002428 -holds_over_chain: RO:0002327 RO:0002211 -holds_over_chain: RO:0002331 RO:0002211 -is_a: RO:0002263 -is_a: RO:0002431 - -[Typedef] -id: RO:0002429 -holds_over_chain: RO:0002327 RO:0002213 -holds_over_chain: RO:0002331 RO:0002213 -is_a: RO:0002428 - -[Typedef] -id: RO:0002430 -holds_over_chain: RO:0002327 RO:0002212 -holds_over_chain: RO:0002331 RO:0002212 -is_a: RO:0002428 - -[Typedef] -id: RO:0002431 -is_a: RO:0002264 -is_a: RO:0002328 -is_a: RO:0002500 - -[Typedef] -id: RO:0002432 -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002131 -is_a: RO:0002328 - -[Typedef] -id: RO:0002434 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_symmetric: true - -[Typedef] -id: RO:0002436 -is_symmetric: true -is_a: RO:0002434 - -[Typedef] -id: RO:0002448 -is_a: RO:0002436 -is_a: RO:0002566 - -[Typedef] -id: RO:0002449 -is_a: RO:0002448 - -[Typedef] -id: RO:0002450 -is_a: RO:0002448 - -[Typedef] -id: RO:0002479 -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} - -[Typedef] -id: RO:0002500 -is_a: RO:0002595 -inverse_of: RO:0002608 - -[Typedef] -id: RO:0002501 -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -is_a: RO:0002410 - -[Typedef] -id: RO:0002506 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002410 - -[Typedef] -id: RO:0002559 -is_a: RO:0002506 -inverse_of: RO:0002566 - -[Typedef] -id: RO:0002566 -is_a: RO:0002506 - -[Typedef] -id: RO:0002578 -is_a: RO:0002211 -is_a: RO:0002412 - -[Typedef] -id: RO:0002584 -holds_over_chain: BFO:0000051 RO:0002215 -is_a: RO:0002328 -is_a: RO:0002595 - -[Typedef] -id: RO:0002595 -domain: BFO:0000040 ! material entity -range: BFO:0000015 ! process -is_a: RO:0002410 - -[Typedef] -id: RO:0002596 -holds_over_chain: RO:0002215 RO:0002211 -is_a: RO:0002500 - -[Typedef] -id: RO:0002597 -holds_over_chain: RO:0002215 RO:0002212 -is_a: RO:0002596 - -[Typedef] -id: RO:0002598 -holds_over_chain: RO:0002215 RO:0002213 -is_a: RO:0002596 - -[Typedef] -id: RO:0002608 -is_a: RO:0002410 - -[Typedef] -id: RO:0002629 -is_a: RO:0002213 -is_a: RO:0002578 - -[Typedef] -id: RO:0002630 -is_a: RO:0002212 -is_a: RO:0002578 - -[Typedef] -id: RO:0004031 -holds_over_chain: RO:0002327 BFO:0000051 -is_a: RO:0002328 - -[Typedef] -id: RO:0004032 -holds_over_chain: RO:0002327 RO:0004047 -is_a: RO:0002264 - -[Typedef] -id: RO:0004033 -holds_over_chain: RO:0002327 RO:0004046 -is_a: RO:0002264 - -[Typedef] -id: RO:0004034 -holds_over_chain: RO:0002327 RO:0002304 -is_a: RO:0002263 -is_a: RO:0004032 - -[Typedef] -id: RO:0004035 -holds_over_chain: RO:0002327 RO:0002305 -is_a: RO:0002263 -is_a: RO:0004033 - -[Typedef] -id: RO:0004046 -is_a: RO:0002418 - -[Typedef] -id: RO:0004047 -is_a: RO:0002418 +ontology: urn:absolute:/imports/ro_import.owl diff --git a/pato.json b/pato.json index aed2d770..266a36c3 100644 --- a/pato.json +++ b/pato.json @@ -6911,6 +6911,46 @@ }, "type" : "CLASS", "lbl" : "obsolete absolute visual ability value" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0040003", + "meta" : { + "definition" : { + "val" : "The ability of a pathogen to produce an infectious disease or disorder in an another organism.", + "xrefs" : [ "https://orcid.org/0000-0001-6330-7526" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-08-02T04:24:52Z" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://orcid.org/0000-0001-5208-3432" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + } ] + }, + "type" : "CLASS", + "lbl" : "pathogenicity" + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0040004", + "meta" : { + "definition" : { + "val" : "A texture quality inhering in a bearer by virtue of the bearer's being covered or partially covered with hair that has increased thickness and softness.", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0003-4606-0597" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://orcid.org/0000-0001-5208-3432" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2018-08-02T04:39:30Z" + } ] + }, + "type" : "CLASS", + "lbl" : "plush" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000820", "meta" : { @@ -8110,41 +8150,41 @@ "type" : "CLASS", "lbl" : "radiation reflective quality" }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001299", + "id" : "http://purl.obolibrary.org/obo/PATO_0002146", "meta" : { "definition" : { - "val" : "A scalar EM radiation quality which obtains by the capacity of the bearer to emit radiation.", - "xrefs" : [ "PATOC:GVG" ] + "val" : "A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism.", + "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0001-8941-3984" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/pato#scalar_slim", "http://purl.obolibrary.org/obo/pato#attribute_slim" ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "george" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-10-30T05:04:06Z" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] }, "type" : "CLASS", - "lbl" : "radiation emitting quality" + "lbl" : "virulence" }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0002146", + "id" : "http://purl.obolibrary.org/obo/PATO_0001299", "meta" : { "definition" : { - "val" : "A quality inhering in a bearer by virtue of the bearer's pathogenicity.", + "val" : "A scalar EM radiation quality which obtains by the capacity of the bearer to emit radiation.", "xrefs" : [ "PATOC:GVG" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#scalar_slim", "http://purl.obolibrary.org/obo/pato#attribute_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "george" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-10-30T05:04:06Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] }, "type" : "CLASS", - "lbl" : "virulence" + "lbl" : "radiation emitting quality" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002147", "meta" : { @@ -46936,10 +46976,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002487", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001236" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000085", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002629", "pred" : "is_a", @@ -47384,10 +47420,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001391", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001389" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001046", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001765", "pred" : "is_a", @@ -49896,6 +49928,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002355", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002353" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0040004", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000150" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002029", "pred" : "is_a", @@ -50268,10 +50304,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000689", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0000077", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001200", "pred" : "is_a", @@ -51464,6 +51496,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001750", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001749" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0001046", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000635", "pred" : "is_a", @@ -51992,6 +52028,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001727", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000077", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001563", "pred" : "is_a", @@ -52880,14 +52920,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002063", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0015011", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0015009" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001685", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001682" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0015011", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0015009" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001227", "pred" : "is_a", @@ -53724,6 +53764,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0045041", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0045040" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0000085", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001919", "pred" : "is_a", @@ -54252,6 +54296,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001574", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001906" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0040003", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0001995" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001613", "pred" : "is_a", @@ -56385,7 +56433,7 @@ "pred" : "http://www.geneontology.org/formats/oboInOwl#saved-by", "val" : "segerdel" } ], - "version" : "http://purl.obolibrary.org/obo/pato/releases/2018-08-09/pato.owl" + "version" : "http://purl.obolibrary.org/obo/pato/releases/2018-08-14/pato.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ { diff --git a/pato.obo b/pato.obo index 3f37f034..596ff0f8 100644 --- a/pato.obo +++ b/pato.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2018-08-09 +data-version: releases/2018-08-14 date: 07:02:2018 10:27 saved-by: segerdel auto-generated-by: OBO-Edit 2.3.1 @@ -526,7 +526,7 @@ subset: scalar_slim synonym: "reactivity" RELATED [GOC:CJM] synonym: "response" RELATED [] synonym: "responsivity" RELATED [] -is_a: PATO:0001018 ! physical quality +is_a: PATO:0001995 ! organismal quality [Term] id: PATO:0000078 @@ -574,7 +574,7 @@ subset: attribute_slim subset: disposition_slim subset: relational_slim synonym: "sensitivity" EXACT [] -is_a: PATO:0001018 ! physical quality +is_a: PATO:0001995 ! organismal quality [Term] id: PATO:0000086 @@ -6506,7 +6506,7 @@ subset: disposition_slim subset: relational_slim subset: scalar_slim synonym: "resistance" EXACT [] -is_a: PATO:0001018 ! physical quality +is_a: PATO:0001995 ! organismal quality relationship: is_opposite_of PATO:0001043 ! susceptibility toward [Term] @@ -15788,7 +15788,7 @@ creation_date: 2009-10-30T03:31:31Z [Term] id: PATO:0002146 name: virulence -def: "A quality inhering in a bearer by virtue of the bearer's pathogenicity." [PATOC:GVG] +def: "A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0001-8941-3984] subset: attribute_slim subset: scalar_slim is_a: PATO:0001995 ! organismal quality @@ -20442,6 +20442,22 @@ is_a: PATO:0000140 ! position property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-5208-3432 property_value: http://purl.org/dc/elements/1.1/date 2018-05-24T04:10:53Z xsd:dateTime +[Term] +id: PATO:0040003 +name: pathogenicity +def: "The ability of a pathogen to produce an infectious disease or disorder in an another organism." [https://orcid.org/0000-0001-6330-7526] +is_a: PATO:0001995 ! organismal quality +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/elements/1.1/date 2018-08-02T04:24:52Z xsd:dateTime + +[Term] +id: PATO:0040004 +name: plush +def: "A texture quality inhering in a bearer by virtue of the bearer's being covered or partially covered with hair that has increased thickness and softness." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0003-4606-0597] +is_a: PATO:0000150 ! texture +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/elements/1.1/date 2018-08-02T04:39:30Z xsd:dateTime + [Term] id: PATO:0045000 name: normal rate diff --git a/pato.owl b/pato.owl index 2cf9f701..b14a5579 100644 --- a/pato.owl +++ b/pato.owl @@ -11,7 +11,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + OBO-Edit 2.3.1 07:02:2018 10:27 quality @@ -1884,7 +1884,7 @@ Association is weaker than correlation or proportionality. These relations may b - + A quality inhering in a bearer by virtue of the whether the bearer's disposition to react to a stimulus or an agent. quality reactivity @@ -2023,7 +2023,7 @@ Association is weaker than correlation or proportionality. These relations may b - + A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation. sensitivity quality @@ -15843,7 +15843,7 @@ Association is weaker than correlation or proportionality. These relations may b - + A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus. resistance @@ -39253,7 +39253,7 @@ Association is weaker than correlation or proportionality. These relations may b - A quality inhering in a bearer by virtue of the bearer's pathogenicity. + A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism. george 2009-10-30T05:04:06Z quality @@ -39265,8 +39265,9 @@ Association is weaker than correlation or proportionality. These relations may b - A quality inhering in a bearer by virtue of the bearer's pathogenicity. - PATOC:GVG + A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism. + https://orcid.org/0000-0001-5208-3432 + https://orcid.org/0000-0001-8941-3984 @@ -50194,6 +50195,47 @@ height'). + + + + + The ability of a pathogen to produce an infectious disease or disorder in an another organism. + + 2018-08-02T04:24:52Z + quality + PATO:0040003 + pathogenicity + + + + + The ability of a pathogen to produce an infectious disease or disorder in an another organism. + https://orcid.org/0000-0001-6330-7526 + + + + + + + + + A texture quality inhering in a bearer by virtue of the bearer's being covered or partially covered with hair that has increased thickness and softness. + + 2018-08-02T04:39:30Z + quality + PATO:0040004 + plush + + + + + A texture quality inhering in a bearer by virtue of the bearer's being covered or partially covered with hair that has increased thickness and softness. + https://orcid.org/0000-0001-5208-3432 + https://orcid.org/0000-0003-4606-0597 + + + +