diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl index 87a298c6..456e39d0 100644 --- a/src/ontology/imports/envo_import.owl +++ b/src/ontology/imports/envo_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( ) Annotation( "http://orcid.org/0000-0002-6601-2165") @@ -26,13 +26,14 @@ Annotation(rdfs:comment "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 40 Logical Axioms: 6]") Annotation(rdfs:comment "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 21 Logical Axioms: 2]") Annotation(owl:versionInfo "2023-02-13") -Annotation(owl:versionInfo "2023-02-19") +Annotation(owl:versionInfo "2023-03-30") Annotation( "http://environmentontology.org/"^^xsd:anyURI) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -121,5 +122,16 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "environmental system") SubClassOf( ) +# Class: (habitat) + +AnnotationAssertion(Annotation( "EnvO:EnvO") "An environmental system which can sustain and allow the growth of an ecological population.") +AnnotationAssertion( "EcoLexicon:habitat") +AnnotationAssertion( "LTER:238") +AnnotationAssertion( "SWEETRealm:Habitat") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Habitat") +AnnotationAssertion(rdfs:comment "A habitat's specificity to an ecological population differentiates it from other environment classes.") +AnnotationAssertion(rdfs:label "habitat"@en) +SubClassOf( ) + ) \ No newline at end of file diff --git a/src/ontology/imports/envo_terms.txt b/src/ontology/imports/envo_terms.txt index 43e38d61..8b37e743 100644 --- a/src/ontology/imports/envo_terms.txt +++ b/src/ontology/imports/envo_terms.txt @@ -1 +1,2 @@ ENVO:01000254 +ENVO:01000739 diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index c8c54f47..ad0fd262 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -1,5 +1,6 @@ Prefix(:=) Prefix(dc:=) +Prefix(dce:=) Prefix(obo:=) Prefix(owl:=) Prefix(rdf:=) @@ -17,6 +18,7 @@ Prefix(oboInOwl:=) Ontology( +Import() Import() Import() Import() @@ -31,24 +33,24 @@ Import() Import() Import() Import() -Annotation(dc:description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."@en) +Annotation(dce:description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."@en) +Annotation(dce:title "OBO Relations Ontology"@en) Annotation(dc:license ) -Annotation(dc:title "OBO Relations Ontology"@en) Annotation(foaf:homepage " https://github.com/oborel/obo-relations/"^^xsd:anyURI) Declaration(Class(obo:BFO_0000019)) Declaration(Class(obo:BFO_0000031)) Declaration(Class(obo:CHEBI_50906)) -Declaration(Class(obo:OGMS_0000031)) +Declaration(Class(obo:CL_0000101)) +Declaration(Class(obo:GO_0004872)) +Declaration(Class(obo:GO_0019107)) Declaration(Class(obo:RO_0002310)) Declaration(Class(obo:RO_0002532)) Declaration(Class(obo:RO_0002533)) Declaration(Class(obo:RO_0002534)) -Declaration(Class(obo:UPHENO_0001001)) Declaration(Class(foaf:image)) Declaration(ObjectProperty(obo:BFO_0000050)) Declaration(ObjectProperty(obo:BFO_0000051)) -Declaration(ObjectProperty(obo:RO_0000058)) Declaration(ObjectProperty(obo:RO_0000300)) Declaration(ObjectProperty(obo:RO_0000301)) Declaration(ObjectProperty(obo:RO_0000302)) @@ -58,7 +60,6 @@ Declaration(ObjectProperty(obo:RO_0001020)) Declaration(ObjectProperty(obo:RO_0001021)) Declaration(ObjectProperty(obo:RO_0001022)) Declaration(ObjectProperty(obo:RO_0001023)) -Declaration(ObjectProperty(obo:RO_0002000)) Declaration(ObjectProperty(obo:RO_0002001)) Declaration(ObjectProperty(obo:RO_0002003)) Declaration(ObjectProperty(obo:RO_0002004)) @@ -84,7 +85,6 @@ Declaration(ObjectProperty(obo:RO_0002023)) Declaration(ObjectProperty(obo:RO_0002024)) Declaration(ObjectProperty(obo:RO_0002025)) Declaration(ObjectProperty(obo:RO_0002026)) -Declaration(ObjectProperty(obo:RO_0002082)) Declaration(ObjectProperty(obo:RO_0002085)) Declaration(ObjectProperty(obo:RO_0002100)) Declaration(ObjectProperty(obo:RO_0002101)) @@ -146,7 +146,6 @@ Declaration(ObjectProperty(obo:RO_0002219)) Declaration(ObjectProperty(obo:RO_0002220)) Declaration(ObjectProperty(obo:RO_0002221)) Declaration(ObjectProperty(obo:RO_0002222)) -Declaration(ObjectProperty(obo:RO_0002223)) Declaration(ObjectProperty(obo:RO_0002225)) Declaration(ObjectProperty(obo:RO_0002226)) Declaration(ObjectProperty(obo:RO_0002227)) @@ -504,6 +503,7 @@ Declaration(ObjectProperty(obo:RO_0008505)) Declaration(ObjectProperty(obo:RO_0008506)) Declaration(ObjectProperty(obo:RO_0008507)) Declaration(ObjectProperty(obo:RO_0008508)) +Declaration(ObjectProperty(obo:RO_0008509)) Declaration(ObjectProperty(obo:RO_0009001)) Declaration(ObjectProperty(obo:RO_0009002)) Declaration(ObjectProperty(obo:RO_0009003)) @@ -567,8 +567,6 @@ Declaration(ObjectProperty(obo:RO_0016001)) Declaration(ObjectProperty(obo:RO_0016002)) Declaration(ObjectProperty(obo:RO_0016004)) Declaration(ObjectProperty(obo:RO_0017001)) -Declaration(ObjectProperty(obo:RO_0017003)) -Declaration(ObjectProperty(obo:RO_0017004)) Declaration(ObjectProperty(obo:RO_0018001)) Declaration(ObjectProperty(obo:RO_0018002)) Declaration(ObjectProperty(obo:RO_0018003)) @@ -592,22 +590,12 @@ Declaration(ObjectProperty(obo:RO_0019002)) Declaration(ObjectProperty(obo:RO_0019501)) Declaration(ObjectProperty(obo:RO_0040035)) Declaration(ObjectProperty(obo:RO_0040036)) -Declaration(ObjectProperty(obo:RO_HOM0000000)) -Declaration(ObjectProperty(obo:RO_HOM0000001)) -Declaration(ObjectProperty(obo:RO_HOM0000003)) Declaration(DataProperty(obo:RO_0002029)) -Declaration(NamedIndividual(obo:RO_0001901)) -Declaration(NamedIndividual(obo:RO_0001902)) -Declaration(AnnotationProperty(obo:IAO_0000111)) Declaration(AnnotationProperty(obo:IAO_0000115)) Declaration(AnnotationProperty(obo:IAO_0000232)) -Declaration(AnnotationProperty(obo:IAO_0000424)) -Declaration(AnnotationProperty(obo:IAO_0000425)) -Declaration(AnnotationProperty(obo:IAO_0000426)) Declaration(AnnotationProperty(obo:IAO_0000589)) Declaration(AnnotationProperty(obo:IAO_0100001)) Declaration(AnnotationProperty(obo:OMO_0002000)) -Declaration(AnnotationProperty(obo:RO_0001900)) Declaration(AnnotationProperty(obo:RO_0002161)) Declaration(AnnotationProperty(obo:RO_0002171)) Declaration(AnnotationProperty(obo:RO_0002172)) @@ -670,10 +658,12 @@ Declaration(AnnotationProperty(obo:valid_for_go_gp2term)) Declaration(AnnotationProperty(obo:valid_for_go_ontology)) Declaration(AnnotationProperty(obo:valid_for_gocam)) Declaration(AnnotationProperty(subsets:ro-eco)) +Declaration(AnnotationProperty(dce:date)) +Declaration(AnnotationProperty(dce:description)) +Declaration(AnnotationProperty(dce:license)) Declaration(AnnotationProperty(dc:conformsTo)) Declaration(AnnotationProperty(dc:contributor)) Declaration(AnnotationProperty(dc:creator)) -Declaration(AnnotationProperty(dc:date)) Declaration(AnnotationProperty(dc:description)) Declaration(AnnotationProperty(dc:license)) Declaration(AnnotationProperty(dc:source)) @@ -694,11 +684,7 @@ Declaration(AnnotationProperty(skos:exactMatch)) # Annotation Properties ############################ -# Annotation Property: obo:IAO_0000112 (example of usage) - -AnnotationAssertion(rdfs:label obo:IAO_0000112 "example of usage") - -# Annotation Property: obo:IAO_0000426 (obo:IAO_0000426) +# Annotation Property: obo:IAO_0000426 (first order logic expression) AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000426 "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.") SubAnnotationPropertyOf(obo:IAO_0000426 obo:RO_0002422) @@ -706,7 +692,6 @@ SubAnnotationPropertyOf(obo:IAO_0000426 obo:RO_0002422) # Annotation Property: obo:RO_0001900 (temporal interpretation) AnnotationAssertion(obo:IAO_0000115 obo:RO_0001900 "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.") -AnnotationAssertion(rdfs:label obo:RO_0001900 "temporal interpretation") AnnotationAssertion(rdfs:seeAlso obo:RO_0001900 ) SubAnnotationPropertyOf(obo:RO_0001900 obo:RO_0002422) @@ -740,8 +725,8 @@ CONSTRUCT { } WHERE { ?x never_in_taxon: ?taxon . -}") -AnnotationAssertion(rdfs:label obo:RO_0002161 "never in taxon") +}"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002161 "never in taxon"^^xsd:string) AnnotationAssertion(rdfs:seeAlso obo:RO_0002161 ) SubAnnotationPropertyOf(obo:RO_0002161 obo:RO_0002172) @@ -770,7 +755,7 @@ CONSTRUCT { } WHERE { ?x mutually_spatially_disjoint_with: ?y . -}") +}"^^xsd:string) AnnotationAssertion(rdfs:label obo:RO_0002171 "mutually spatially disjoint with"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0002171 obo:RO_0002163) AnnotationAssertion(rdfs:seeAlso obo:RO_0002171 "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"^^xsd:anyURI) @@ -828,7 +813,7 @@ WHERE { MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label) -}") +}"^^xsd:string) AnnotationAssertion(rdfs:comment obo:RO_0002175 "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.") AnnotationAssertion(rdfs:label obo:RO_0002175 "present in taxon"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0002175 ) @@ -1150,7 +1135,7 @@ SubAnnotationPropertyOf(obo:RO_0002617 obo:RO_0002601) # Annotation Property: obo:RO_0004036 (nominally disjoint with) AnnotationAssertion(obo:IAO_0000115 obo:RO_0004036 "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation.") -AnnotationAssertion(dc:creator obo:RO_0004036 ) +AnnotationAssertion(dce:creator obo:RO_0004036 ) AnnotationAssertion(rdfs:label obo:RO_0004036 "nominally disjoint with"@en) SubAnnotationPropertyOf(obo:RO_0004036 obo:RO_0002422) @@ -1189,7 +1174,7 @@ SubAnnotationPropertyOf(obo:RO_0040042 obo:RO_0002422) # Annotation Property: obo:valid_for_go_annotation_extension (valid_for_go_annotation_extension) -AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_annotation_extension ) +AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_annotation_extension "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:valid_for_go_annotation_extension "2020-09-22T11:05:29Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:valid_for_go_annotation_extension "valid_for_go_annotation_extension"@en) AnnotationAssertion(rdfs:seeAlso obo:valid_for_go_annotation_extension ) @@ -1197,7 +1182,7 @@ SubAnnotationPropertyOf(obo:valid_for_go_annotation_extension oboInOwl:SubsetPro # Annotation Property: obo:valid_for_go_gp2term (valid_for_go_gp2term) -AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_gp2term ) +AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_gp2term "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:valid_for_go_gp2term "2020-09-22T11:05:18Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:valid_for_go_gp2term "valid_for_go_gp2term"@en) AnnotationAssertion(rdfs:seeAlso obo:valid_for_go_gp2term ) @@ -1205,7 +1190,7 @@ SubAnnotationPropertyOf(obo:valid_for_go_gp2term oboInOwl:SubsetProperty) # Annotation Property: obo:valid_for_go_ontology (valid_for_go_ontology) -AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_ontology ) +AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_ontology "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:valid_for_go_ontology "2020-09-22T11:04:12Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:valid_for_go_ontology "valid_for_go_ontology"@en) AnnotationAssertion(rdfs:seeAlso obo:valid_for_go_ontology ) @@ -1213,7 +1198,7 @@ SubAnnotationPropertyOf(obo:valid_for_go_ontology oboInOwl:SubsetProperty) # Annotation Property: obo:valid_for_gocam (valid_for_gocam) -AnnotationAssertion(oboInOwl:created_by obo:valid_for_gocam ) +AnnotationAssertion(oboInOwl:created_by obo:valid_for_gocam "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:valid_for_gocam "2020-09-22T11:05:45Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:valid_for_gocam "valid_for_gocam"@en) AnnotationAssertion(rdfs:seeAlso obo:valid_for_gocam ) @@ -1227,15 +1212,15 @@ SubAnnotationPropertyOf(subsets:ro-eco oboInOwl:SubsetProperty) # Annotation Property: oboInOwl:SubsetProperty (subset_property) -AnnotationAssertion(rdfs:label oboInOwl:SubsetProperty "subset_property") +AnnotationAssertion(rdfs:label oboInOwl:SubsetProperty "subset_property"^^xsd:string) # Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) -AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") +AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym"^^xsd:string) # Annotation Property: oboInOwl:inSubset (in_subset) -AnnotationAssertion(rdfs:label oboInOwl:inSubset "in_subset") +AnnotationAssertion(rdfs:label oboInOwl:inSubset "in_subset"^^xsd:string) ############################ @@ -1257,7 +1242,6 @@ AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000050 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000050 obo:valid_for_gocam) AnnotationAssertion(rdfs:seeAlso obo:BFO_0000050 ) AnnotationAssertion(rdfs:seeAlso obo:BFO_0000050 ) -AnnotationAssertion(rdfs:seeAlso obo:BFO_0000050 ) SubObjectPropertyOf(obo:BFO_0000050 obo:RO_0002131) # Object Property: obo:BFO_0000051 (has part) @@ -1281,7 +1265,6 @@ SubObjectPropertyOf(obo:BFO_0000063 obo:RO_0002222) AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000066 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000066 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:BFO_0000066 obo:valid_for_gocam) -AnnotationAssertion(rdfs:seeAlso obo:BFO_0000066 ) # Object Property: obo:RO_0000052 (characteristic of) @@ -1382,7 +1365,6 @@ ObjectPropertyRange(obo:RO_0001023 obo:BFO_0000040) # Object Property: obo:RO_0001025 (located in) AnnotationAssertion(oboInOwl:inSubset obo:RO_0001025 obo:valid_for_go_gp2term) -AnnotationAssertion(rdfs:seeAlso obo:RO_0001025 ) # Object Property: obo:RO_0002000 (2D boundary of) @@ -1408,17 +1390,17 @@ SubObjectPropertyOf(obo:RO_0002002 obo:RO_0002323) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002003 "A relation that holds between two neurons that are electrically coupled via gap junctions.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002003 ) AnnotationAssertion(cito:citesAsAuthority obo:RO_0002003 ) -AnnotationAssertion(rdfs:label obo:RO_0002003 "electrically_synapsed_to") +AnnotationAssertion(rdfs:label obo:RO_0002003 "electrically_synapsed_to"^^xsd:string) SubObjectPropertyOf(obo:RO_0002003 obo:RO_0002170) # Object Property: obo:RO_0002004 (tracheates) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002004 "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002004 "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)."^^xsd:string) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002004 ) AnnotationAssertion(rdfs:label obo:RO_0002004 "tracheates"@en) SubObjectPropertyOf(obo:RO_0002004 obo:RO_0001018) -ObjectPropertyDomain(obo:RO_0002004 obo:UBERON_0000061) -ObjectPropertyRange(obo:RO_0002004 obo:UBERON_0000061) +ObjectPropertyDomain(obo:RO_0002004 obo:CARO_0000003) +ObjectPropertyRange(obo:RO_0002004 obo:CARO_0000003) # Object Property: obo:RO_0002005 (innervated_by) @@ -1426,8 +1408,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002005 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002008 subsets:ro-eco) @@ -1510,7 +1492,7 @@ ObjectPropertyRange(obo:RO_0002012 obo:BFO_0000003) # Object Property: obo:RO_0002013 (has regulatory component activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002013 "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002013 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002013 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002013 "2017-05-24T09:30:46Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002013 "has regulatory component activity") SubObjectPropertyOf(obo:RO_0002013 obo:RO_0002017) @@ -1519,7 +1501,7 @@ SubObjectPropertyOf(obo:RO_0002013 obo:RO_0002334) # Object Property: obo:RO_0002014 (has negative regulatory component activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002014 "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002014 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002014 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002014 "2017-05-24T09:31:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002014 "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") AnnotationAssertion(rdfs:label obo:RO_0002014 "has negative regulatory component activity") @@ -1529,7 +1511,7 @@ SubObjectPropertyOf(obo:RO_0002014 obo:RO_0002335) # Object Property: obo:RO_0002015 (has positive regulatory component activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002015 "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002015 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002015 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002015 "2017-05-24T09:31:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002015 "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") AnnotationAssertion(rdfs:label obo:RO_0002015 "has positive regulatory component activity") @@ -1538,7 +1520,7 @@ SubObjectPropertyOf(obo:RO_0002015 obo:RO_0002336) # Object Property: obo:RO_0002016 (has necessary component activity) -AnnotationAssertion(oboInOwl:created_by obo:RO_0002016 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002016 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002016 "2017-05-24T09:36:08Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002016 "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.") AnnotationAssertion(rdfs:label obo:RO_0002016 "has necessary component activity") @@ -1547,7 +1529,7 @@ SubObjectPropertyOf(obo:RO_0002016 obo:RO_0002336) # Object Property: obo:RO_0002017 (has component activity) -AnnotationAssertion(oboInOwl:created_by obo:RO_0002017 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002017 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002017 "2017-05-24T09:44:33Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002017 "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") AnnotationAssertion(rdfs:label obo:RO_0002017 "has component activity") @@ -1556,7 +1538,7 @@ SubObjectPropertyOf(obo:RO_0002017 obo:RO_0002018) # Object Property: obo:RO_0002018 (has component process) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002018 "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002018 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002018 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002018 "2017-05-24T09:49:21Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002018 "has component process") SubObjectPropertyOf(obo:RO_0002018 obo:RO_0002180) @@ -1566,7 +1548,7 @@ ObjectPropertyRange(obo:RO_0002018 obo:BFO_0000015) # Object Property: obo:RO_0002019 (has ligand) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002019 "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002019 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002019 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002019 "2017-07-19T17:30:36Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002019 "has ligand") SubObjectPropertyOf(obo:RO_0002019 obo:RO_0002233) @@ -1574,7 +1556,7 @@ SubObjectPropertyOf(obo:RO_0002019 obo:RO_0002233) # Object Property: obo:RO_0002020 (transports) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002020 "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002020 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002020 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002020 "2017-07-20T17:11:08Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002020 "transports") SubObjectPropertyOf(obo:RO_0002020 obo:RO_0002313) @@ -1582,24 +1564,24 @@ SubObjectPropertyOf(obo:RO_0002020 obo:RO_0002313) # Object Property: obo:RO_0002021 (occurs across) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002021 "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002021 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002021 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002021 "2017-07-20T17:19:37Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002021 "occurs across") SubObjectPropertyOf(obo:RO_0002021 obo:RO_0002479) # Object Property: obo:RO_0002022 (directly regulated by) -AnnotationAssertion(oboInOwl:created_by obo:RO_0002022 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002022 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002022 "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) rdfs:comment obo:RO_0002022 "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) rdfs:comment obo:RO_0002022 "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") AnnotationAssertion(rdfs:label obo:RO_0002022 "directly regulated by") SubObjectPropertyOf(obo:RO_0002022 obo:RO_0002334) InverseObjectProperties(obo:RO_0002022 obo:RO_0002578) # Object Property: obo:RO_0002023 (directly negatively regulated by) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) obo:IAO_0000115 obo:RO_0002023 "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002023 ) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002023 "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") +AnnotationAssertion(oboInOwl:created_by obo:RO_0002023 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002023 "2017-09-17T13:52:38Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002023 "directly negatively regulated by") SubObjectPropertyOf(obo:RO_0002023 obo:RO_0002022) @@ -1607,8 +1589,8 @@ InverseObjectProperties(obo:RO_0002023 obo:RO_0002630) # Object Property: obo:RO_0002024 (directly positively regulated by) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) obo:IAO_0000115 obo:RO_0002024 "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002024 ) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002024 "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") +AnnotationAssertion(oboInOwl:created_by obo:RO_0002024 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002024 "2017-09-17T13:52:47Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002024 "directly positively regulated by") SubObjectPropertyOf(obo:RO_0002024 obo:RO_0002022) @@ -1616,8 +1598,8 @@ InverseObjectProperties(obo:RO_0002024 obo:RO_0002629) # Object Property: obo:RO_0002025 (has effector activity) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) obo:IAO_0000115 obo:RO_0002025 "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002025 ) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002025 "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") +AnnotationAssertion(oboInOwl:created_by obo:RO_0002025 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002025 "2017-09-22T14:14:36Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002025 "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") AnnotationAssertion(rdfs:label obo:RO_0002025 "has effector activity") @@ -1626,7 +1608,7 @@ FunctionalObjectProperty(obo:RO_0002025) # Object Property: obo:RO_0002026 (in register with) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) obo:IAO_0000115 obo:RO_0002026 "A relationship that holds between two images, A and B, where: +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002026 "A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' @@ -1634,7 +1616,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002026 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002026 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002026 "2017-12-07T12:58:06Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002026 "in register with"@en) SubObjectPropertyOf(obo:RO_0002026 obo:RO_0002323) @@ -1643,10 +1625,8 @@ ObjectPropertyRange(obo:RO_0002026 foaf:image) # Object Property: obo:RO_0002082 (simultaneous with) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002082 "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002082 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002082 subsets:ro-eco) -SymmetricObjectProperty(obo:RO_0002082) # Object Property: obo:RO_0002085 (encompasses) @@ -1678,13 +1658,12 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002092 obo:valid_for_go_annotation AnnotationAssertion(oboInOwl:inSubset obo:RO_0002092 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002092 obo:valid_for_gocam) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002092 subsets:ro-eco) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002092 ) SubObjectPropertyOf(obo:RO_0002092 obo:RO_0002091) # Object Property: obo:RO_0002100 (has soma location) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002100 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002100 "Relation between a neuron and a material anatomical entity that its soma is part of."@en) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002100 "Relation between a neuron and an anatomical structure that its soma is part of."@en) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002100 ) AnnotationAssertion(obo:IAO_0000424 obo:RO_0002100 " some ( and some ?Y)") @@ -1692,7 +1671,7 @@ AnnotationAssertion(obo:RO_0001900 obo:RO_0002100 obo:RO_0001901) AnnotationAssertion(rdfs:label obo:RO_0002100 "has soma location"@en) SubObjectPropertyOf(obo:RO_0002100 obo:RO_0002131) ObjectPropertyDomain(obo:RO_0002100 obo:CL_0000540) -ObjectPropertyRange(obo:RO_0002100 obo:UBERON_0000465) +ObjectPropertyRange(obo:RO_0002100 obo:CARO_0000003) # Object Property: obo:RO_0002101 (fasciculates with) @@ -1720,14 +1699,14 @@ AnnotationAssertion(obo:IAO_0000426 obo:RO_0002101 "(forall (?x ?y) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) - ))))))") + ))))))"^^xsd:string) AnnotationAssertion(obo:RO_0001900 obo:RO_0002101 obo:RO_0001901) AnnotationAssertion(cito:citesAsAuthority obo:RO_0002101 ) AnnotationAssertion(rdfs:label obo:RO_0002101 "fasciculates with"@en) SubObjectPropertyOf(obo:RO_0002101 obo:RO_0002131) InverseObjectProperties(obo:RO_0002101 obo:RO_0002132) ObjectPropertyDomain(obo:RO_0002101 obo:CL_0000540) -ObjectPropertyRange(obo:RO_0002101 obo:UBERON_0000122) +ObjectPropertyRange(obo:RO_0002101 obo:CARO_0001001) # Object Property: obo:RO_0002102 (axon synapses in) @@ -1772,8 +1751,8 @@ AnnotationAssertion(obo:IAO_0000424 obo:RO_0002104 ") AnnotationAssertion(rdfs:label obo:RO_0002132 "has fasciculating neuron projection"@en) SubObjectPropertyOf(obo:RO_0002132 obo:RO_0002131) -ObjectPropertyDomain(obo:RO_0002132 obo:UBERON_0000122) +ObjectPropertyDomain(obo:RO_0002132 obo:CARO_0001001) ObjectPropertyRange(obo:RO_0002132 ObjectUnionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:BFO_0000050 obo:CL_0000540))) # Object Property: obo:RO_0002134 (innervates) @@ -2027,12 +2006,12 @@ AnnotationAssertion(obo:IAO_0000424 obo:RO_0002134 ") AnnotationAssertion(rdfs:label obo:RO_0002134 "innervates"@en) -ObjectPropertyDomain(obo:RO_0002134 obo:UBERON_0000122) +ObjectPropertyDomain(obo:RO_0002134 obo:CARO_0001001) # Object Property: obo:RO_0002150 (continuous with) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002150 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002150 "X continuous_with Y if and only if X and Y share a fiat boundary.") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002150 "X continuous_with Y if and only if X and Y share a fiat boundary."^^xsd:string) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002150 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002150 "connected to") AnnotationAssertion(obo:IAO_0000232 obo:RO_0002150 "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)") @@ -2049,14 +2028,14 @@ ObjectPropertyRange(obo:RO_0002150 obo:BFO_0000004) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002151 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002151 "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") AnnotationAssertion(obo:IAO_0000116 obo:RO_0002151 "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") -AnnotationAssertion(obo:IAO_0000118 obo:RO_0002151 "proper overlaps") +AnnotationAssertion(obo:IAO_0000118 obo:RO_0002151 "proper overlaps"^^xsd:string) AnnotationAssertion(obo:IAO_0000426 obo:RO_0002151 "(forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) - (not (part_of ?y ?x)))))") + (not (part_of ?y ?x)))))"^^xsd:string) AnnotationAssertion(obo:RO_0001900 obo:RO_0002151 obo:RO_0001901) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002151 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002151 "partially overlaps"@en) @@ -2065,10 +2044,10 @@ SubObjectPropertyOf(obo:RO_0002151 obo:RO_0002131) # Object Property: obo:RO_0002156 (derived by descent from) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002156 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002156 "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.") -AnnotationAssertion(obo:IAO_0000118 obo:RO_0002156 "ancestral_stucture_of") -AnnotationAssertion(obo:IAO_0000118 obo:RO_0002156 "evolutionarily_descended_from") -AnnotationAssertion(rdfs:label obo:RO_0002156 "derived by descent from") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002156 "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a."^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:RO_0002156 "ancestral_stucture_of"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:RO_0002156 "evolutionarily_descended_from"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002156 "derived by descent from"^^xsd:string) SubObjectPropertyOf(obo:RO_0002156 obo:RO_0002320) InverseObjectProperties(obo:RO_0002156 obo:RO_0002157) TransitiveObjectProperty(obo:RO_0002156) @@ -2078,17 +2057,17 @@ TransitiveObjectProperty(obo:RO_0002156) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002157 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002157 "inverse of derived by descent from") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002157 obo:RO_0002259) -AnnotationAssertion(rdfs:label obo:RO_0002157 "has derived by descendant") +AnnotationAssertion(rdfs:label obo:RO_0002157 "has derived by descendant"^^xsd:string) SubObjectPropertyOf(obo:RO_0002157 obo:RO_0002320) TransitiveObjectProperty(obo:RO_0002157) # Object Property: obo:RO_0002158 (shares ancestor with) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002158 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002158 "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002158 "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a."^^xsd:string) AnnotationAssertion(obo:IAO_0000232 obo:RO_0002158 "Consider obsoleting and merging with child relation, 'in homology relationship with'") -AnnotationAssertion(rdfs:comment obo:RO_0002158 "VBO calls this homologous_to") -AnnotationAssertion(rdfs:label obo:RO_0002158 "shares ancestor with") +AnnotationAssertion(rdfs:comment obo:RO_0002158 "VBO calls this homologous_to"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002158 "shares ancestor with"^^xsd:string) SubObjectPropertyOf(obo:RO_0002158 obo:RO_0002320) SymmetricObjectProperty(obo:RO_0002158) TransitiveObjectProperty(obo:RO_0002158) @@ -2096,7 +2075,7 @@ TransitiveObjectProperty(obo:RO_0002158) # Object Property: obo:RO_0002159 (serially homologous to) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002159 obo:IAO_0000125) -AnnotationAssertion(rdfs:label obo:RO_0002159 "serially homologous to") +AnnotationAssertion(rdfs:label obo:RO_0002159 "serially homologous to"^^xsd:string) SubObjectPropertyOf(obo:RO_0002159 obo:RO_0002320) SymmetricObjectProperty(obo:RO_0002159) TransitiveObjectProperty(obo:RO_0002159) @@ -2112,7 +2091,7 @@ AnnotationAssertion(obo:IAO_0000116 obo:RO_0002160 "The original intent was to t AnnotationAssertion(obo:IAO_0000117 obo:RO_0002160 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002160 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002160 ) -AnnotationAssertion(rdfs:label obo:RO_0002160 "only in taxon") +AnnotationAssertion(rdfs:label obo:RO_0002160 "only in taxon"^^xsd:string) AnnotationAssertion(rdfs:seeAlso obo:RO_0002160 ) SubObjectPropertyOf(obo:RO_0002160 obo:RO_0002162) @@ -2125,11 +2104,11 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002162 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002162 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002162 subsets:ro-eco) -AnnotationAssertion(rdfs:comment obo:RO_0002162 "Connects a biological entity to its taxon of origin.") -AnnotationAssertion(rdfs:label obo:RO_0002162 "in taxon") +AnnotationAssertion(rdfs:comment obo:RO_0002162 "Connects a biological entity to its taxon of origin."^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002162 "in taxon"^^xsd:string) AnnotationAssertion(rdfs:seeAlso obo:RO_0002162 ) SubObjectPropertyOf(obo:RO_0002162 obo:RO_0002320) -ObjectPropertyRange(obo:RO_0002162 obo:OBI_0100026) +ObjectPropertyRange(obo:RO_0002162 obo:CARO_0001010) # Object Property: obo:RO_0002163 (spatially disjoint from) @@ -2142,7 +2121,7 @@ AnnotationAssertion(obo:IAO_0000232 obo:RO_0002163 "Note that it would be possib AnnotationAssertion(obo:IAO_0000424 obo:RO_0002163 "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)") AnnotationAssertion(obo:RO_0001900 obo:RO_0002163 obo:RO_0001901) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002163 subsets:ro-eco) -AnnotationAssertion(rdfs:label obo:RO_0002163 "spatially disjoint from") +AnnotationAssertion(rdfs:label obo:RO_0002163 "spatially disjoint from"^^xsd:string) AnnotationAssertion(rdfs:seeAlso obo:RO_0002163 "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002163 obo:RO_0002323) @@ -2178,8 +2157,8 @@ AnnotationAssertion(obo:IAO_0000589 obo:RO_0002177 "attached to part of (anatomi AnnotationAssertion(rdfs:label obo:RO_0002177 "attached to part of"@en) SubObjectPropertyOf(obo:RO_0002177 obo:RO_0002323) SubObjectPropertyOf(obo:RO_0002177 obo:RO_0002567) -ObjectPropertyDomain(obo:RO_0002177 obo:UBERON_0000061) -ObjectPropertyRange(obo:RO_0002177 obo:UBERON_0000061) +ObjectPropertyDomain(obo:RO_0002177 obo:CARO_0000003) +ObjectPropertyRange(obo:RO_0002177 obo:CARO_0000003) # Object Property: obo:RO_0002178 (supplies) @@ -2218,7 +2197,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002200 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002200 "has phenotype"@en) SubObjectPropertyOf(obo:RO_0002200 obo:RO_0016001) InverseObjectProperties(obo:RO_0002200 obo:RO_0002201) -ObjectPropertyDomain(obo:RO_0002200 ObjectUnionOf(obo:BFO_0000031 obo:OGMS_0000031 obo:UBERON_0000465)) +ObjectPropertyDomain(obo:RO_0002200 ObjectUnionOf(obo:BFO_0000031 obo:CARO_0000006 obo:OGMS_0000031)) ObjectPropertyRange(obo:RO_0002200 obo:UPHENO_0001001) # Object Property: obo:RO_0002201 (phenotype of) @@ -2298,7 +2277,7 @@ SubObjectPropertyOf(obo:RO_0002206 obo:RO_0002330) InverseObjectProperties(obo:RO_0002206 obo:RO_0002292) ObjectPropertyDomain(obo:RO_0002206 obo:BFO_0000002) ObjectPropertyDomain(obo:RO_0002206 ObjectUnionOf(obo:BFO_0000031 obo:BFO_0000040)) -ObjectPropertyRange(obo:RO_0002206 obo:UBERON_0000465) +ObjectPropertyRange(obo:RO_0002206 obo:CARO_0000006) # Object Property: obo:RO_0002207 (directly develops from) @@ -2306,15 +2285,15 @@ AnnotationAssertion(obo:IAO_0000114 obo:RO_0002207 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002207 "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.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002207 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002207 ) +AnnotationAssertion(obo:IAO_0000117 obo:RO_0002207 "has developmental precursor") AnnotationAssertion(obo:IAO_0000119 obo:RO_0002207 "FBbt") AnnotationAssertion(obo:RO_0002575 obo:RO_0002207 obo:RO_0002202) -AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002207 "has developmental precursor") AnnotationAssertion(rdfs:comment obo:RO_0002207 "TODO - add child relations from DOS") AnnotationAssertion(rdfs:label obo:RO_0002207 "directly develops from"@en) SubObjectPropertyOf(obo:RO_0002207 obo:RO_0002202) InverseObjectProperties(obo:RO_0002207 obo:RO_0002210) -ObjectPropertyDomain(obo:RO_0002207 ObjectUnionOf(obo:CL_0000000 obo:UBERON_0010000)) -ObjectPropertyRange(obo:RO_0002207 ObjectUnionOf(obo:CL_0000000 obo:UBERON_0010000)) +ObjectPropertyDomain(obo:RO_0002207 ObjectUnionOf(obo:CARO_0010000 obo:CL_0000000)) +ObjectPropertyRange(obo:RO_0002207 ObjectUnionOf(obo:CARO_0010000 obo:CL_0000000)) # Object Property: obo:RO_0002208 (parasitoid of) @@ -2436,8 +2415,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002217 "OBSOLETE x actively particip AnnotationAssertion(obo:IAO_0000117 obo:RO_0002217 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002217 "agent in") AnnotationAssertion(obo:IAO_0100001 obo:RO_0002217 obo:RO_0002608) -AnnotationAssertion(rdfs:comment obo:RO_0002217 "Obsoleted as the inverse property was obsoleted.") -AnnotationAssertion(rdfs:label obo:RO_0002217 "obsolete actively participates in") +AnnotationAssertion(rdfs:comment obo:RO_0002217 "Obsoleted as the inverse property was obsoleted."^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002217 "obsolete actively participates in"^^xsd:string) AnnotationAssertion(owl:deprecated obo:RO_0002217 "true"^^xsd:boolean) # Object Property: obo:RO_0002218 (obsolete has active participant) @@ -2446,7 +2425,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002218 "OBSOLETE x has participant y AnnotationAssertion(obo:IAO_0000117 obo:RO_0002218 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002218 "has agent") AnnotationAssertion(obo:IAO_0100001 obo:RO_0002218 obo:RO_0002500) -AnnotationAssertion(rdfs:label obo:RO_0002218 "obsolete has active participant") +AnnotationAssertion(rdfs:label obo:RO_0002218 "obsolete has active participant"^^xsd:string) AnnotationAssertion(owl:deprecated obo:RO_0002218 "true"^^xsd:boolean) # Object Property: obo:RO_0002219 (surrounded by) @@ -2524,7 +2503,7 @@ AnnotationAssertion(obo:IAO_0000119 obo:RO_0002226 "EHDAA2") AnnotationAssertion(obo:IAO_0000119 obo:RO_0002226 "Jonathan Bard, EHDAA2") AnnotationAssertion(rdfs:label obo:RO_0002226 "develops in"@en) SubObjectPropertyOf(obo:RO_0002226 obo:RO_0002258) -ObjectPropertyDomain(obo:RO_0002226 obo:UBERON_0001062) +ObjectPropertyDomain(obo:RO_0002226 obo:CARO_0000000) # Object Property: obo:RO_0002227 (obligate parasite of) @@ -2585,7 +2564,6 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002233 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002233 obo:valid_for_gocam) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002233 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002233 "has input"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002233 ) SubObjectPropertyOf(obo:RO_0002233 obo:RO_0000057) InverseObjectProperties(obo:RO_0002233 obo:RO_0002352) ObjectPropertyDomain(obo:RO_0002233 obo:BFO_0000015) @@ -2601,7 +2579,6 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002234 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002234 obo:valid_for_gocam) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002234 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002234 "has output"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002234 ) SubObjectPropertyOf(obo:RO_0002234 obo:RO_0000057) InverseObjectProperties(obo:RO_0002234 obo:RO_0002353) @@ -2728,8 +2705,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002254 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002264 ) SubObjectPropertyOf(obo:RO_0002264 obo:RO_0002500) # Object Property: obo:RO_0002285 (developmentally replaces) @@ -2859,7 +2817,7 @@ InverseObjectProperties(obo:RO_0002291 obo:RO_0002293) # Object Property: obo:RO_0002292 (expresses) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002292 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002292 "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002292 "Inverse of 'expressed in'") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002292 ) AnnotationAssertion(rdfs:label obo:RO_0002292 "expresses"@en) SubObjectPropertyOf(obo:RO_0002292 obo:RO_0002330) @@ -2883,7 +2841,7 @@ AnnotationAssertion(rdfs:label obo:RO_0002295 "results in developmental progress AnnotationAssertion(rdfs:seeAlso obo:RO_0002295 ) SubObjectPropertyOf(obo:RO_0002295 obo:RO_0002324) ObjectPropertyDomain(obo:RO_0002295 obo:GO_0008150) -ObjectPropertyRange(obo:RO_0002295 obo:UBERON_0001062) +ObjectPropertyRange(obo:RO_0002295 obo:CARO_0000000) # Object Property: obo:RO_0002296 (results in development of) @@ -2984,7 +2942,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002303 subsets:ro-eco) AnnotationAssertion(rdfs:comment obo:RO_0002303 "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.") AnnotationAssertion(rdfs:label obo:RO_0002303 "has habitat"@en) SubObjectPropertyOf(obo:RO_0002303 obo:RO_0002321) -ObjectPropertyDomain(obo:RO_0002303 obo:OBI_0100026) +ObjectPropertyDomain(obo:RO_0002303 obo:CARO_0001010) ObjectPropertyRange(obo:RO_0002303 obo:ENVO_01000254) # Object Property: obo:RO_0002304 (causally upstream of, positive effect) @@ -2996,7 +2954,6 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002304 obo:valid_for_go_annotation AnnotationAssertion(oboInOwl:inSubset obo:RO_0002304 obo:valid_for_gocam) AnnotationAssertion(rdfs:comment obo:RO_0002304 "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") AnnotationAssertion(rdfs:label obo:RO_0002304 "causally upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso obo:RO_0002304 ) SubObjectPropertyOf(obo:RO_0002304 obo:RO_0002411) SubObjectPropertyOf(obo:RO_0002304 obo:RO_0004047) @@ -3008,7 +2965,6 @@ AnnotationAssertion(dc:creator obo:RO_0002305 ) SubObjectPropertyOf(obo:RO_0002305 obo:RO_0002411) SubObjectPropertyOf(obo:RO_0002305 obo:RO_0004046) @@ -3065,7 +3021,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002315 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0002315 "results in acquisition of features of"@en) SubObjectPropertyOf(obo:RO_0002315 obo:RO_0002295) SubObjectPropertyOf(obo:RO_0002315 obo:RO_0040036) -ObjectPropertyRange(obo:RO_0002315 obo:UBERON_0000061) +ObjectPropertyRange(obo:RO_0002315 obo:CARO_0000003) # Object Property: obo:RO_0002320 (evolutionarily related to) @@ -3140,7 +3096,6 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002326 ) SubObjectPropertyOf(obo:RO_0002326 obo:RO_0002216) SubObjectPropertyOf(obo:RO_0002326 obo:RO_0002329) @@ -3157,7 +3112,6 @@ AnnotationAssertion(obo:IAO_0000118 obo:RO_0002327 "is executing") AnnotationAssertion(obo:IAO_0000232 obo:RO_0002327 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002327 obo:valid_for_go_gp2term) AnnotationAssertion(rdfs:label obo:RO_0002327 "enables"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002327 ) SubObjectPropertyOf(obo:RO_0002327 obo:RO_0002215) InverseObjectProperties(obo:RO_0002327 obo:RO_0002333) @@ -3193,7 +3147,6 @@ AnnotationAssertion(obo:IAO_0000118 obo:RO_0002331 "actively involved in") AnnotationAssertion(obo:IAO_0000118 obo:RO_0002331 "enables part of") AnnotationAssertion(rdfs:label obo:RO_0002331 "involved in"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0002331 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002331 ) SubObjectPropertyOf(obo:RO_0002331 obo:RO_0000056) SubObjectPropertyOf(obo:RO_0002331 obo:RO_0002431) @@ -3215,7 +3168,6 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002333 "inverse of enables") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002333 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002333 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0002333 "enabled by"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002333 ) SubObjectPropertyOf(obo:RO_0002333 obo:RO_0000057) SubObjectPropertyOf(obo:RO_0002333 obo:RO_0002328) @@ -3317,7 +3269,7 @@ SubObjectPropertyOf(obo:RO_0002344 obo:RO_0002337) # Object Property: obo:RO_0002345 (exports) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002345 "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002345 "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s."^^xsd:string) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002345 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002345 obo:valid_for_go_ontology) AnnotationAssertion(rdfs:label obo:RO_0002345 "exports"@en) @@ -3425,7 +3377,7 @@ AnnotationAssertion(rdfs:label obo:RO_0002372 "has muscle origin"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0002372 ) SubObjectPropertyOf(obo:RO_0002372 obo:RO_0002371) SubObjectPropertyOf(obo:RO_0002372 obo:RO_0002567) -ObjectPropertyDomain(Annotation(rdfs:comment "We need to import uberon muscle to create a stricter domain constraint") obo:RO_0002372 obo:UBERON_0000061) +ObjectPropertyDomain(Annotation(rdfs:comment "We need to import uberon muscle to create a stricter domain constraint") obo:RO_0002372 obo:CARO_0000003) # Object Property: obo:RO_0002373 (has muscle insertion) @@ -3436,7 +3388,7 @@ AnnotationAssertion(rdfs:label obo:RO_0002373 "has muscle insertion"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0002373 ) SubObjectPropertyOf(obo:RO_0002373 obo:RO_0002371) SubObjectPropertyOf(obo:RO_0002373 obo:RO_0002567) -ObjectPropertyDomain(Annotation(obo:IAO_0000116 "We need to import uberon muscle into RO to use as a stricter domain constraint") obo:RO_0002373 obo:UBERON_0000061) +ObjectPropertyDomain(Annotation(obo:IAO_0000116 "We need to import uberon muscle into RO to use as a stricter domain constraint") obo:RO_0002373 obo:CARO_0000003) # Object Property: obo:RO_0002374 (derived from ancestral fusion of) @@ -3573,8 +3525,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002384 "x has developmental potentia AnnotationAssertion(obo:IAO_0000117 obo:RO_0002384 ) AnnotationAssertion(rdfs:label obo:RO_0002384 "has developmental potential involving"@en) SubObjectPropertyOf(obo:RO_0002384 obo:RO_0002324) -ObjectPropertyDomain(obo:RO_0002384 obo:UBERON_0001062) -ObjectPropertyRange(obo:RO_0002384 obo:UBERON_0001062) +ObjectPropertyDomain(obo:RO_0002384 obo:CARO_0000000) +ObjectPropertyRange(obo:RO_0002384 obo:CARO_0000000) # Object Property: obo:RO_0002385 (has potential to developmentally contribute to) @@ -3625,7 +3577,7 @@ AnnotationAssertion(obo:IAO_0000114 obo:RO_0002401 obo:IAO_0000428) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002401 ) AnnotationAssertion(rdfs:comment obo:RO_0002401 "Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit") -AnnotationAssertion(rdfs:label obo:RO_0002401 "obsolete has indirect input") +AnnotationAssertion(rdfs:label obo:RO_0002401 "obsolete has indirect input"^^xsd:string) AnnotationAssertion(owl:deprecated obo:RO_0002401 "true"^^xsd:boolean) # Object Property: obo:RO_0002402 (obsolete has direct output) @@ -3635,7 +3587,7 @@ AnnotationAssertion(obo:IAO_0000114 obo:RO_0002402 obo:IAO_0000428) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002402 "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. ") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002402 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002402 "directly produces") -AnnotationAssertion(rdfs:label obo:RO_0002402 "obsolete has direct output") +AnnotationAssertion(rdfs:label obo:RO_0002402 "obsolete has direct output"^^xsd:string) AnnotationAssertion(owl:deprecated obo:RO_0002402 "true"^^xsd:boolean) # Object Property: obo:RO_0002403 (obsolete has indirect output) @@ -3644,7 +3596,7 @@ AnnotationAssertion(obo:IAO_0000114 obo:RO_0002403 obo:IAO_0000428) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002403 ) AnnotationAssertion(rdfs:comment obo:RO_0002403 "Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit") -AnnotationAssertion(rdfs:label obo:RO_0002403 "obsolete has indirect output") +AnnotationAssertion(rdfs:label obo:RO_0002403 "obsolete has indirect output"^^xsd:string) AnnotationAssertion(owl:deprecated obo:RO_0002403 "true"^^xsd:boolean) # Object Property: obo:RO_0002404 (causally downstream of) @@ -3669,7 +3621,7 @@ InverseObjectProperties(obo:RO_0002405 obo:RO_0002412) # Object Property: obo:RO_0002406 (obsolete directly activates) AnnotationAssertion(obo:IAO_0100001 obo:RO_0002406 obo:RO_0002629) -AnnotationAssertion(rdfs:comment obo:RO_0002406 "This term was obsoleted because it has the same meaning as 'directly positively regulates'.") +AnnotationAssertion(rdfs:comment obo:RO_0002406 "This term was obsoleted because it has the same meaning as 'directly positively regulates'."^^xsd:string) AnnotationAssertion(rdfs:label obo:RO_0002406 "obsolete directly activates"@en) AnnotationAssertion(owl:deprecated obo:RO_0002406 "true"^^xsd:boolean) @@ -3680,7 +3632,6 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002407 ) SubObjectPropertyOf(obo:RO_0002407 obo:RO_0002213) SubObjectPropertyOf(obo:RO_0002407 obo:RO_0012012) TransitiveObjectProperty(obo:RO_0002407) @@ -3688,7 +3639,7 @@ TransitiveObjectProperty(obo:RO_0002407) # Object Property: obo:RO_0002408 (obsolete directly inhibits) AnnotationAssertion(obo:IAO_0100001 obo:RO_0002408 obo:RO_0002630) -AnnotationAssertion(rdfs:comment obo:RO_0002408 "This term was obsoleted because it has the same meaning as 'directly negatively regulates'.") +AnnotationAssertion(rdfs:comment obo:RO_0002408 "This term was obsoleted because it has the same meaning as 'directly negatively regulates'."^^xsd:string) AnnotationAssertion(rdfs:label obo:RO_0002408 "obsolete directly inhibits"@en) AnnotationAssertion(owl:deprecated obo:RO_0002408 "true"^^xsd:boolean) @@ -3699,7 +3650,6 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002409 ) SubObjectPropertyOf(obo:RO_0002409 obo:RO_0002212) SubObjectPropertyOf(obo:RO_0002409 obo:RO_0012012) TransitiveObjectProperty(obo:RO_0002409) @@ -3749,12 +3699,12 @@ SubObjectPropertyOf(obo:RO_0002412 obo:RO_0002411) # Object Property: obo:RO_0002413 (provides input for) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002413 "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.") +AnnotationAssertion(obo:IAO_0000116 obo:RO_0002413 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002413 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002413 "directly provides input for") AnnotationAssertion(obo:IAO_0000119 obo:RO_0002413 ) AnnotationAssertion(obo:IAO_0000589 obo:RO_0002413 "directly provides input for (process to process)") AnnotationAssertion(rdfs:label obo:RO_0002413 "provides input for"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0002413 ) SubObjectPropertyOf(obo:RO_0002413 obo:RO_0002412) SubObjectPropertyOf(obo:RO_0002413 obo:RO_0002414) @@ -3853,13 +3803,12 @@ SubObjectPropertyOf(obo:RO_0002431 obo:RO_0002500) # Object Property: obo:RO_0002432 (is active in) AnnotationAssertion(obo:IAO_0000112 obo:RO_0002432 "A protein that enables activity in a cytosol.") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref ) obo:IAO_0000115 obo:RO_0002432 "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cjm"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002432 "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002432 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002432 "executes activity in") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002432 "enables activity in") AnnotationAssertion(rdfs:comment obo:RO_0002432 "") AnnotationAssertion(rdfs:label obo:RO_0002432 "is active in") -AnnotationAssertion(rdfs:seeAlso obo:RO_0002432 ) SubObjectPropertyOf(obo:RO_0002432 obo:RO_0002131) SubObjectPropertyOf(obo:RO_0002432 obo:RO_0002328) @@ -3873,8 +3822,8 @@ SubObjectPropertyOf(obo:RO_0002433 obo:RO_0002131) # Object Property: obo:RO_0002434 (interacts with) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002434 "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) +AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002434 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0002434 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002434 "in pairwise interaction with") @@ -4367,9 +4316,9 @@ SubObjectPropertyOf(obo:RO_0002490 obo:RO_0002487) # Object Property: obo:RO_0002491 (existence starts and ends during) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002491 "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002491 "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)"^^xsd:string) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002491 ) -AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002491 "exists during") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002491 "exists during"^^xsd:string) AnnotationAssertion(rdfs:comment obo:RO_0002491 "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label obo:RO_0002491 "existence starts and ends during") SubObjectPropertyOf(obo:RO_0002491 obo:RO_0002488) @@ -4775,8 +4724,8 @@ SubObjectPropertyOf(obo:RO_0002551 obo:BFO_0000051) InverseObjectProperties(obo:RO_0002551 obo:RO_0002576) AsymmetricObjectProperty(obo:RO_0002551) IrreflexiveObjectProperty(obo:RO_0002551) -ObjectPropertyDomain(obo:RO_0002551 obo:UBERON_0000061) -ObjectPropertyRange(Annotation(obo:IAO_0000116 "This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.") obo:RO_0002551 obo:UBERON_0000465) +ObjectPropertyDomain(obo:RO_0002551 obo:CARO_0000003) +ObjectPropertyRange(Annotation(obo:IAO_0000116 "This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.") obo:RO_0002551 obo:CARO_0000006) # Object Property: obo:RO_0002552 (results in ending of) @@ -4901,8 +4850,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002567 ) -AnnotationAssertion(obo:IAO_0000119 obo:RO_0002571 ) +AnnotationAssertion(obo:IAO_0000119 obo:RO_0002571 "GOC:cjm") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002571 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002571 "lumen of") SubObjectPropertyOf(obo:RO_0002571 obo:BFO_0000050) @@ -4972,8 +4921,8 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002574 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002574 "participates in a biotic-biotic interaction with") AnnotationAssertion(rdfs:seeAlso obo:RO_0002574 ) SubObjectPropertyOf(obo:RO_0002574 obo:RO_0002437) -ObjectPropertyDomain(obo:RO_0002574 obo:OBI_0100026) -ObjectPropertyRange(obo:RO_0002574 obo:OBI_0100026) +ObjectPropertyDomain(obo:RO_0002574 obo:CARO_0001010) +ObjectPropertyRange(obo:RO_0002574 obo:CARO_0001010) # Object Property: obo:RO_0002576 (skeleton of) @@ -4982,8 +4931,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:RO_0002576 ) SubObjectPropertyOf(obo:RO_0002629 obo:RO_0002213) SubObjectPropertyOf(obo:RO_0002629 obo:RO_0002578) @@ -5251,7 +5199,6 @@ AnnotationAssertion(oboInOwl:inSubset obo:RO_0002630 obo:valid_for_go_annotation AnnotationAssertion(oboInOwl:inSubset obo:RO_0002630 obo:valid_for_go_ontology) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002630 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0002630 "directly negatively regulates") -AnnotationAssertion(rdfs:seeAlso obo:RO_0002630 ) SubObjectPropertyOf(obo:RO_0002630 obo:RO_0002212) SubObjectPropertyOf(obo:RO_0002630 obo:RO_0002578) @@ -5339,10 +5286,10 @@ SymmetricObjectProperty(obo:RO_0002801) # Object Property: obo:RO_0003000 (produces) AnnotationAssertion(obo:IAO_0000114 obo:RO_0003000 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0003000 "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003000 "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix."^^xsd:string) AnnotationAssertion(obo:IAO_0000117 obo:RO_0003000 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0003000 subsets:ro-eco) -AnnotationAssertion(rdfs:comment obo:RO_0003000 "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") +AnnotationAssertion(rdfs:comment obo:RO_0003000 "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue."^^xsd:string) AnnotationAssertion(rdfs:label obo:RO_0003000 "produces"@en) InverseObjectProperties(obo:RO_0003000 obo:RO_0003001) ObjectPropertyDomain(obo:RO_0003000 obo:BFO_0000040) @@ -5533,7 +5480,7 @@ SubObjectPropertyOf(obo:RO_0004007 obo:RO_0000057) # Object Property: obo:RO_0004008 (has primary output) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref "GOC:dph") Annotation(oboInOwl:hasDbXref "GOC:kva") Annotation(oboInOwl:hasDbXref "GOC:pt") Annotation(rdfs:comment "PMID:27812932") obo:IAO_0000115 obo:RO_0004008 "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cjm"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:dph"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:kva") Annotation(oboInOwl:hasDbXref "GOC:pt") Annotation(rdfs:comment "PMID:27812932") obo:IAO_0000115 obo:RO_0004008 "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.") AnnotationAssertion(oboInOwl:created_by obo:RO_0004008 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0004008 "2018-12-13T11:26:32Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0004008 obo:valid_for_go_ontology) @@ -5543,7 +5490,7 @@ SubObjectPropertyOf(obo:RO_0004008 obo:RO_0004007) # Object Property: obo:RO_0004009 (has primary input) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref "GOC:dph") Annotation(oboInOwl:hasDbXref "GOC:kva") Annotation(oboInOwl:hasDbXref "GOC:pt") Annotation(rdfs:comment "PMID:27812932") obo:IAO_0000115 obo:RO_0004009 "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cjm"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:dph"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:kva") Annotation(oboInOwl:hasDbXref "GOC:pt") Annotation(rdfs:comment "PMID:27812932") obo:IAO_0000115 obo:RO_0004009 "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.") AnnotationAssertion(oboInOwl:created_by obo:RO_0004009 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0004009 "2018-12-13T11:26:56Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0004009 obo:valid_for_go_ontology) @@ -5649,7 +5596,7 @@ AnnotationAssertion(oboInOwl:created_by obo:RO_0004020 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0004032 ) SubObjectPropertyOf(obo:RO_0004032 obo:RO_0002264) # Object Property: obo:RO_0004033 (acts upstream of or within, negative effect) @@ -5782,7 +5728,6 @@ AnnotationAssertion(oboInOwl:created_by obo:RO_0004033 ) SubObjectPropertyOf(obo:RO_0004033 obo:RO_0002264) # Object Property: obo:RO_0004034 (acts upstream of, positive effect) @@ -5794,7 +5739,6 @@ AnnotationAssertion(oboInOwl:creation_date obo:RO_0004034 "2018-01-26T23:53:14Z" AnnotationAssertion(oboInOwl:inSubset obo:RO_0004034 obo:valid_for_go_gp2term) AnnotationAssertion(rdfs:label obo:RO_0004034 "acts upstream of, positive effect") AnnotationAssertion(rdfs:seeAlso obo:RO_0004034 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0004034 ) SubObjectPropertyOf(obo:RO_0004034 obo:RO_0002263) SubObjectPropertyOf(obo:RO_0004034 obo:RO_0004032) @@ -5807,7 +5751,6 @@ AnnotationAssertion(oboInOwl:creation_date obo:RO_0004035 "2018-01-26T23:53:22Z" AnnotationAssertion(oboInOwl:inSubset obo:RO_0004035 obo:valid_for_go_gp2term) AnnotationAssertion(rdfs:label obo:RO_0004035 "acts upstream of, negative effect") AnnotationAssertion(rdfs:seeAlso obo:RO_0004035 ) -AnnotationAssertion(rdfs:seeAlso obo:RO_0004035 ) SubObjectPropertyOf(obo:RO_0004035 obo:RO_0002263) SubObjectPropertyOf(obo:RO_0004035 obo:RO_0004033) @@ -5817,7 +5760,6 @@ AnnotationAssertion(obo:RO_0004050 obo:RO_0004046 obo:RO_0002418) AnnotationAssertion(oboInOwl:created_by obo:RO_0004046 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0004046 "2018-03-13T23:55:05Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0004046 "causally upstream of or within, negative effect") -AnnotationAssertion(rdfs:seeAlso obo:RO_0004046 ) SubObjectPropertyOf(obo:RO_0004046 obo:RO_0002418) # Object Property: obo:RO_0004047 (causally upstream of or within, positive effect) @@ -5826,7 +5768,6 @@ AnnotationAssertion(obo:RO_0004049 obo:RO_0004047 obo:RO_0002418) AnnotationAssertion(oboInOwl:created_by obo:RO_0004047 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0004047 "2018-03-13T23:55:19Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0004047 "causally upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso obo:RO_0004047 ) SubObjectPropertyOf(obo:RO_0004047 obo:RO_0002418) # Object Property: obo:RO_0007000 (has driver) @@ -5879,8 +5820,8 @@ SubObjectPropertyOf(obo:RO_0008504 obo:RO_0002445) AnnotationAssertion(obo:IAO_0000115 obo:RO_0008505 "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.") AnnotationAssertion(rdfs:label obo:RO_0008505 "creates habitat for") SubObjectPropertyOf(obo:RO_0008505 obo:RO_0002321) -ObjectPropertyDomain(obo:RO_0008505 obo:OBI_0100026) -ObjectPropertyRange(obo:RO_0008505 obo:OBI_0100026) +ObjectPropertyDomain(obo:RO_0008505 obo:CARO_0001010) +ObjectPropertyRange(obo:RO_0008505 obo:CARO_0001010) # Object Property: obo:RO_0008506 (ecologically co-occurs with) @@ -5888,8 +5829,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0008506 "An interaction relationship AnnotationAssertion(rdfs:label obo:RO_0008506 "ecologically co-occurs with") SubObjectPropertyOf(obo:RO_0008506 obo:RO_0002321) SymmetricObjectProperty(obo:RO_0008506) -ObjectPropertyDomain(obo:RO_0008506 obo:OBI_0100026) -ObjectPropertyRange(obo:RO_0008506 obo:OBI_0100026) +ObjectPropertyDomain(obo:RO_0008506 obo:CARO_0001010) +ObjectPropertyRange(obo:RO_0008506 obo:CARO_0001010) # Object Property: obo:RO_0008507 (lays eggs on) @@ -5904,6 +5845,17 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0008508 "inverse of lays eggs on") AnnotationAssertion(rdfs:label obo:RO_0008508 "has eggs laid on by") SubObjectPropertyOf(obo:RO_0008508 obo:RO_0002619) +# Object Property: obo:RO_0008509 (has roost) + +AnnotationAssertion(obo:IAO_0000112 obo:RO_0008509 "Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis)") +AnnotationAssertion(obo:IAO_0000115 obo:RO_0008509 "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x.") +AnnotationAssertion(dce:creator obo:RO_0008509 ) +AnnotationAssertion(dce:date obo:RO_0008509 "2023-01-18T14:28:21Z"^^xsd:dateTime) +AnnotationAssertion(oboInOwl:inSubset obo:RO_0008509 subsets:ro-eco) +AnnotationAssertion(rdfs:comment obo:RO_0008509 "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y.") +AnnotationAssertion(rdfs:label obo:RO_0008509 "has roost"@en) +SubObjectPropertyOf(obo:RO_0008509 obo:RO_0002303) + # Object Property: obo:RO_0009001 (has substance added) AnnotationAssertion(obo:IAO_0000112 obo:RO_0009001 "muffin 'has substance added' some 'baking soda'"@en) @@ -5946,7 +5898,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0009004 "'has consumer' is a relation AnnotationAssertion(obo:IAO_0000117 obo:RO_0009004 ) AnnotationAssertion(rdfs:label obo:RO_0009004 "has consumer"@en) ObjectPropertyDomain(obo:RO_0009004 obo:BFO_0000040) -ObjectPropertyRange(obo:RO_0009004 obo:OBI_0100026) +ObjectPropertyRange(obo:RO_0009004 obo:CARO_0001010) # Object Property: obo:RO_0009005 (has primary substance added) @@ -5968,7 +5920,7 @@ AnnotationAssertion(dc:contributor obo:RO_0009501 ) AnnotationAssertion(dc:contributor obo:RO_0009501 ) AnnotationAssertion(dc:contributor obo:RO_0009501 ) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) oboInOwl:hasExactSynonym obo:RO_0009501 "triggered by process") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "RO:cjm") oboInOwl:hasExactSynonym obo:RO_0009501 "triggered by process") AnnotationAssertion(rdfs:label obo:RO_0009501 "realized in response to"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0009501 "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0009501 obo:RO_0002410) @@ -6136,8 +6088,8 @@ SubObjectPropertyOf(obo:RO_0011024 obo:RO_0011022) # Object Property: obo:RO_0012000 (has small molecule regulator) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012000 "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012000 ) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012000 "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012000 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012000 "2020-04-22T20:27:26Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012000 "has small molecule regulator"@en) SubObjectPropertyOf(obo:RO_0012000 obo:RO_0000057) @@ -6145,8 +6097,8 @@ InverseObjectProperties(obo:RO_0012000 obo:RO_0012004) # Object Property: obo:RO_0012001 (has small molecule activator) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012001 "a relation between a process and a continuant, in which the process is activated by the small molecule continuant") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012001 ) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012001 "a relation between a process and a continuant, in which the process is activated by the small molecule continuant"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012001 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012001 "2020-04-22T20:28:37Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012001 "has small molecule activator"@en) SubObjectPropertyOf(obo:RO_0012001 obo:RO_0012000) @@ -6154,8 +6106,8 @@ InverseObjectProperties(obo:RO_0012001 obo:RO_0012005) # Object Property: obo:RO_0012002 (has small molecule inhibitor) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012002 "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012002 ) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012002 "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012002 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012002 "2020-04-22T20:28:54Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012002 "has small molecule inhibitor"@en) SubObjectPropertyOf(obo:RO_0012002 obo:RO_0012000) @@ -6163,8 +6115,8 @@ InverseObjectProperties(obo:RO_0012002 obo:RO_0012006) # Object Property: obo:RO_0012003 (acts on population of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012003 "p acts on population of c iff c' is a collection, has members of type c, and p has participant c") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012003 ) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012003 "p acts on population of c iff c' is a collection, has members of type c, and p has participant c"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012003 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012003 "2020-06-08T17:21:33Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012003 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012003 obo:valid_for_go_ontology) @@ -6174,43 +6126,41 @@ SubObjectPropertyOf(obo:RO_0012003 obo:RO_0000057) # Object Property: obo:RO_0012004 (is small molecule regulator of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012004 "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012004 ) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012004 "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012004 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012004 "2020-06-24T13:15:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012004 "is small molecule regulator of"@en) SubObjectPropertyOf(obo:RO_0012004 obo:RO_0002596) # Object Property: obo:RO_0012005 (is small molecule activator of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012005 "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012005 ) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012005 "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012005 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012005 "2020-06-24T13:15:26Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012005 "is small molecule activator of"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0012005 ) SubObjectPropertyOf(obo:RO_0012005 obo:RO_0002598) SubObjectPropertyOf(obo:RO_0012005 obo:RO_0012004) # Object Property: obo:RO_0012006 (is small molecule inhibitor of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012006 "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012006 ) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012006 "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012006 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012006 "2020-06-24T13:15:35Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012006 "is small molecule inhibitor of"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0012006 ) SubObjectPropertyOf(obo:RO_0012006 obo:RO_0002597) SubObjectPropertyOf(obo:RO_0012006 obo:RO_0012004) # Object Property: obo:RO_0012007 (results in adhesion of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012007 "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012007 ) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012007 "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities."^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012007 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012007 "2020-08-27T08:13:59Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012007 "results in adhesion of"@en) SubObjectPropertyOf(obo:RO_0012007 obo:RO_0040036) # Object Property: obo:RO_0012008 (results in fusion of) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012008 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012008 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012008 "2021-02-26T07:28:29Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012008 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012008 obo:valid_for_go_ontology) @@ -6221,29 +6171,27 @@ SubObjectPropertyOf(obo:RO_0012008 obo:RO_0002592) # Object Property: obo:RO_0012009 (constitutively upstream of) AnnotationAssertion(obo:IAO_0000115 obo:RO_0012009 "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012009 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012009 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012009 "2022-09-26T06:01:01Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012009 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012009 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0012009 "constitutively upstream of"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0012009 ) SubObjectPropertyOf(obo:RO_0012009 obo:RO_0002304) # Object Property: obo:RO_0012010 (removes input for) AnnotationAssertion(obo:IAO_0000115 obo:RO_0012010 "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012010 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012010 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012010 "2022-09-26T06:06:20Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012010 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012010 obo:valid_for_gocam) AnnotationAssertion(rdfs:label obo:RO_0012010 "removes input for"@en) -AnnotationAssertion(rdfs:seeAlso obo:RO_0012010 ) SubObjectPropertyOf(obo:RO_0012010 obo:RO_0002305) # Object Property: obo:RO_0012011 (indirectly causally upstream of) AnnotationAssertion(obo:IAO_0000115 obo:RO_0012011 "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012011 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012011 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012011 "2022-09-26T06:07:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012011 "indirectly causally upstream of"@en) SubObjectPropertyOf(obo:RO_0012011 obo:RO_0002411) @@ -6251,7 +6199,7 @@ SubObjectPropertyOf(obo:RO_0012011 obo:RO_0002411) # Object Property: obo:RO_0012012 (indirectly regulates) AnnotationAssertion(obo:IAO_0000115 obo:RO_0012012 "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012012 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012012 "pg"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0012012 "2022-09-26T06:08:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012012 "indirectly regulates"@en) SubObjectPropertyOf(obo:RO_0012012 obo:RO_0002211) @@ -6260,7 +6208,7 @@ SubObjectPropertyOf(obo:RO_0012012 obo:RO_0012011) # Object Property: obo:RO_0013001 (has synaptic IO in region) AnnotationAssertion(obo:IAO_0000115 obo:RO_0013001 "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0013001 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0013001 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0013001 "2020-07-17T09:26:52Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0013001 "has synaptic input or output in") AnnotationAssertion(rdfs:label obo:RO_0013001 "has synaptic IO in region"@en) @@ -6269,7 +6217,7 @@ SubObjectPropertyOf(obo:RO_0013001 obo:RO_0002130) # Object Property: obo:RO_0013002 (receives synaptic input in region) AnnotationAssertion(obo:IAO_0000115 obo:RO_0013002 "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0013002 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0013002 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0013002 "2020-07-17T09:42:23Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0013002 "receives synaptic input in region"@en) SubObjectPropertyOf(obo:RO_0013002 obo:RO_0002110) @@ -6278,7 +6226,7 @@ SubObjectPropertyOf(obo:RO_0013002 obo:RO_0013001) # Object Property: obo:RO_0013003 (sends synaptic output to region) AnnotationAssertion(obo:IAO_0000115 obo:RO_0013003 "A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0013003 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0013003 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0013003 "2020-07-17T09:45:06Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0013003 "sends synaptic output to region"@en) SubObjectPropertyOf(obo:RO_0013003 obo:RO_0002113) @@ -6287,7 +6235,7 @@ SubObjectPropertyOf(obo:RO_0013003 obo:RO_0013001) # Object Property: obo:RO_0013004 (has synaptic IO throughout) AnnotationAssertion(obo:IAO_0000115 obo:RO_0013004 "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).") -AnnotationAssertion(oboInOwl:created_by obo:RO_0013004 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0013004 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0013004 "2020-07-17T09:52:19Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0013004 "has synaptic IO throughout"@en) SubObjectPropertyOf(obo:RO_0013004 obo:RO_0013001) @@ -6295,7 +6243,7 @@ SubObjectPropertyOf(obo:RO_0013004 obo:RO_0013001) # Object Property: obo:RO_0013005 (receives synaptic input throughout) AnnotationAssertion(obo:IAO_0000115 obo:RO_0013005 "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).") -AnnotationAssertion(oboInOwl:created_by obo:RO_0013005 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0013005 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0013005 "2020-07-17T09:55:36Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0013005 "receives synaptic input throughout"@en) SubObjectPropertyOf(obo:RO_0013005 obo:RO_0013002) @@ -6304,7 +6252,7 @@ SubObjectPropertyOf(obo:RO_0013005 obo:RO_0013004) # Object Property: obo:RO_0013006 (sends synaptic output throughout) AnnotationAssertion(obo:IAO_0000115 obo:RO_0013006 "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).") -AnnotationAssertion(oboInOwl:created_by obo:RO_0013006 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0013006 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0013006 "2020-07-17T09:57:27Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0013006 "sends synaptic output throughout"@en) SubObjectPropertyOf(obo:RO_0013006 obo:RO_0013003) @@ -6313,7 +6261,7 @@ SubObjectPropertyOf(obo:RO_0013006 obo:RO_0013004) # Object Property: obo:RO_0013007 (has sensory dendrite in) AnnotationAssertion(obo:IAO_0000115 obo:RO_0013007 "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0013007 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0013007 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0013007 "2020-07-20T12:10:09Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0013007 "has sensory dendrite location") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0013007 "has sensory terminal in") @@ -6325,7 +6273,7 @@ ObjectPropertyDomain(obo:RO_0013007 obo:CL_0000101) # Object Property: obo:RO_0013008 (receives synaptic input from neuron) AnnotationAssertion(obo:IAO_0000115 obo:RO_0013008 "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0013008 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0013008 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0013008 "2021-05-26T08:40:18Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0013008 "receives synaptic input from neuron"@en) SubObjectPropertyOf(obo:RO_0013008 obo:RO_0002103) @@ -6334,7 +6282,7 @@ InverseObjectProperties(obo:RO_0013008 obo:RO_0013009) # Object Property: obo:RO_0013009 (sends synaptic output to cell) AnnotationAssertion(obo:IAO_0000115 obo:RO_0013009 "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0013009 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0013009 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0013009 "2021-05-26T08:41:07Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0013009 "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron.") AnnotationAssertion(rdfs:label obo:RO_0013009 "sends synaptic output to cell"@en) @@ -6343,7 +6291,7 @@ SubObjectPropertyOf(obo:RO_0013009 obo:RO_0002120) # Object Property: obo:RO_0014001 (disease has infectious agent) AnnotationAssertion(obo:IAO_0000115 obo:RO_0014001 "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0014001 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0014001 ) AnnotationAssertion(rdfs:label obo:RO_0014001 "disease has infectious agent") SubObjectPropertyOf(obo:RO_0014001 obo:RO_0004019) @@ -6381,7 +6329,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:RO_0015004 "transcriptomically defined c AnnotationAssertion(obo:IAO_0000115 obo:RO_0015004 "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type.") AnnotationAssertion(obo:IAO_0000116 obo:RO_0015004 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types.") AnnotationAssertion(obo:IAO_0000232 obo:RO_0015004 "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context.") -AnnotationAssertion(dc:contributor obo:RO_0015004 ) +AnnotationAssertion(dce:contributor obo:RO_0015004 ) AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0015004 "has marker gene combination") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0015004 "has marker signature set") AnnotationAssertion(rdfs:label obo:RO_0015004 "has characterizing marker set") @@ -6397,7 +6345,7 @@ ObjectPropertyRange(obo:RO_0015006 obo:PATO_0000001) # Object Property: obo:RO_0015007 (increased in magnitude relative to) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-6601-2165") obo:IAO_0000115 obo:RO_0015007 "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") -AnnotationAssertion(rdfs:comment obo:RO_0015007 "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.") +AnnotationAssertion(rdfs:comment obo:RO_0015007 "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'."^^xsd:string) AnnotationAssertion(rdfs:label obo:RO_0015007 "increased in magnitude relative to") SubObjectPropertyOf(obo:RO_0015007 obo:RO_0015006) ObjectPropertyDomain(obo:RO_0015007 obo:PATO_0000001) @@ -6406,7 +6354,7 @@ ObjectPropertyRange(obo:RO_0015007 obo:PATO_0000001) # Object Property: obo:RO_0015008 (decreased in magnitude relative to) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-6601-2165") obo:IAO_0000115 obo:RO_0015008 "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") -AnnotationAssertion(rdfs:comment obo:RO_0015008 "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.") +AnnotationAssertion(rdfs:comment obo:RO_0015008 "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'."^^xsd:string) AnnotationAssertion(rdfs:label obo:RO_0015008 "decreased in magnitude relative to") SubObjectPropertyOf(obo:RO_0015008 obo:RO_0015006) ObjectPropertyDomain(obo:RO_0015008 obo:PATO_0000001) @@ -6424,21 +6372,21 @@ AnnotationAssertion(rdfs:label obo:RO_0015010 "has relative magnitude") # Object Property: obo:RO_0015011 (has cross section) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-6601-2165") obo:IAO_0000115 obo:RO_0015011 "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.") -AnnotationAssertion(rdfs:comment obo:RO_0015011 "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.") +AnnotationAssertion(rdfs:comment obo:RO_0015011 "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round."^^xsd:string) AnnotationAssertion(rdfs:label obo:RO_0015011 "has cross section") # Object Property: obo:RO_0015012 (reciprocal of) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-6601-2165") obo:IAO_0000115 obo:RO_0015012 "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.") -AnnotationAssertion(rdfs:comment obo:RO_0015012 "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.") +AnnotationAssertion(rdfs:comment obo:RO_0015012 "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality."^^xsd:string) AnnotationAssertion(rdfs:label obo:RO_0015012 "reciprocal of") # Object Property: obo:RO_0015015 (has high plasma membrane amount) AnnotationAssertion(obo:IAO_0000112 obo:RO_0015015 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19243617") obo:IAO_0000115 obo:RO_0015015 "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.") -AnnotationAssertion(dc:contributor obo:RO_0015015 ) -AnnotationAssertion(dc:contributor obo:RO_0015015 ) +AnnotationAssertion(dc:contributor obo:RO_0015015 ) +AnnotationAssertion(dc:contributor obo:RO_0015015 ) AnnotationAssertion(rdfs:label obo:RO_0015015 "has high plasma membrane amount") SubObjectPropertyOf(obo:RO_0015015 obo:RO_0002104) ObjectPropertyDomain(obo:RO_0015015 obo:CL_0000000) @@ -6447,8 +6395,8 @@ ObjectPropertyDomain(obo:RO_0015015 obo:CL_0000000) AnnotationAssertion(obo:IAO_0000112 obo:RO_0015016 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19243617") obo:IAO_0000115 obo:RO_0015016 "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.") -AnnotationAssertion(dc:contributor obo:RO_0015016 ) -AnnotationAssertion(dc:contributor obo:RO_0015016 ) +AnnotationAssertion(dc:contributor obo:RO_0015016 ) +AnnotationAssertion(dc:contributor obo:RO_0015016 ) AnnotationAssertion(rdfs:label obo:RO_0015016 "has low plasma membrane amount") SubObjectPropertyOf(obo:RO_0015016 obo:RO_0002104) ObjectPropertyDomain(obo:RO_0015016 obo:CL_0000000) @@ -6456,16 +6404,16 @@ ObjectPropertyDomain(obo:RO_0015016 obo:CL_0000000) # Object Property: obo:RO_0016001 (has phenotype or disease) AnnotationAssertion(obo:IAO_0000232 obo:RO_0016001 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease.") -AnnotationAssertion(dc:contributor obo:RO_0016001 ) -AnnotationAssertion(dc:date obo:RO_0016001 "2021-11-05T17:30:14Z"^^xsd:dateTime) +AnnotationAssertion(dce:contributor obo:RO_0016001 ) +AnnotationAssertion(dce:date obo:RO_0016001 "2021-11-05T17:30:14Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0016001 "has phenotype or disease") AnnotationAssertion(rdfs:seeAlso obo:RO_0016001 "https://github.com/oborel/obo-relations/issues/478") # Object Property: obo:RO_0016002 (has disease) AnnotationAssertion(obo:IAO_0000115 obo:RO_0016002 "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.") -AnnotationAssertion(dc:contributor obo:RO_0016002 ) -AnnotationAssertion(dc:date obo:RO_0016002 "2021-11-05T17:30:44Z"^^xsd:dateTime) +AnnotationAssertion(dce:contributor obo:RO_0016002 ) +AnnotationAssertion(dce:date obo:RO_0016002 "2021-11-05T17:30:44Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0016002 "has disease") AnnotationAssertion(rdfs:seeAlso obo:RO_0016002 "https://github.com/oborel/obo-relations/issues/478") SubObjectPropertyOf(obo:RO_0016002 obo:RO_0016001) @@ -6474,7 +6422,7 @@ SubObjectPropertyOf(obo:RO_0016002 obo:RO_0016001) AnnotationAssertion(obo:IAO_0000115 obo:RO_0016004 "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y.") AnnotationAssertion(obo:IAO_0000119 obo:RO_0016004 "ExO:0000083") -AnnotationAssertion(dc:date obo:RO_0016004 "2021-12-14T20:41:45Z"^^xsd:dateTime) +AnnotationAssertion(dce:date obo:RO_0016004 "2021-12-14T20:41:45Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:created_by obo:RO_0016004 ) AnnotationAssertion(rdfs:label obo:RO_0016004 "has exposure medium") SubObjectPropertyOf(obo:RO_0016004 obo:RO_0002244) @@ -6491,26 +6439,6 @@ AnnotationAssertion(oboInOwl:creation_date obo:RO_0017001 "2021-11-08T12:00:00Z" AnnotationAssertion(oboInOwl:hasBroadSynonym obo:RO_0017001 "utilizes") AnnotationAssertion(rdfs:label obo:RO_0017001 "device utilizes material"@en) -# Object Property: obo:RO_0017003 (positively correlated with) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0017003 "A relation between entities in which one increases or decreases as the other does the same."@en) -AnnotationAssertion(obo:IAO_0000118 obo:RO_0017003 "directly correlated with"@en) -AnnotationAssertion(dc:contributor obo:RO_0017003 ) -AnnotationAssertion(rdfs:label obo:RO_0017003 "positively correlated with"@en) -SubObjectPropertyOf(obo:RO_0017003 obo:RO_0002610) -SymmetricObjectProperty(obo:RO_0017003) -ReflexiveObjectProperty(obo:RO_0017003) - -# Object Property: obo:RO_0017004 (negatively correlated with) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0017004 "A relation between entities in which one increases as the other decreases."@en) -AnnotationAssertion(obo:IAO_0000118 obo:RO_0017004 "inversely correlated with"@en) -AnnotationAssertion(dc:contributor obo:RO_0017004 ) -AnnotationAssertion(rdfs:label obo:RO_0017004 "negatively correlated with"@en) -SubObjectPropertyOf(obo:RO_0017004 obo:RO_0002610) -SymmetricObjectProperty(obo:RO_0017004) -IrreflexiveObjectProperty(obo:RO_0017004) - # Object Property: obo:RO_0018001 (is myristoyltransferase activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0018001 "Helper relation for OWL definition of RO:0018002 myristoylates") @@ -6537,7 +6465,7 @@ AnnotationAssertion(rdfs:label obo:RO_0018003 "myristoylated by") AnnotationAssertion(obo:IAO_0000112 obo:RO_0018027 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)") AnnotationAssertion(obo:IAO_0000115 obo:RO_0018027 "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor") -AnnotationAssertion(dc:creator obo:RO_0018027 ) +AnnotationAssertion(dce:creator obo:RO_0018027 ) AnnotationAssertion(rdfs:label obo:RO_0018027 "is agonist of") AnnotationAssertion(rdfs:seeAlso obo:RO_0018027 ) SubObjectPropertyOf(obo:RO_0018027 obo:RO_0002450) @@ -6546,7 +6474,7 @@ SubObjectPropertyOf(obo:RO_0018027 obo:RO_0002450) AnnotationAssertion(obo:IAO_0000112 obo:RO_0018028 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)") AnnotationAssertion(obo:IAO_0000115 obo:RO_0018028 "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level") -AnnotationAssertion(dc:creator obo:RO_0018028 ) +AnnotationAssertion(dce:creator obo:RO_0018028 ) AnnotationAssertion(rdfs:label obo:RO_0018028 "is inverse agonist of") AnnotationAssertion(rdfs:seeAlso obo:RO_0018028 ) SubObjectPropertyOf(obo:RO_0018028 obo:RO_0002449) @@ -6555,7 +6483,7 @@ SubObjectPropertyOf(obo:RO_0018028 obo:RO_0002449) AnnotationAssertion(obo:IAO_0000112 obo:RO_0018029 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)") AnnotationAssertion(obo:IAO_0000115 obo:RO_0018029 "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level") -AnnotationAssertion(dc:creator obo:RO_0018029 ) +AnnotationAssertion(dce:creator obo:RO_0018029 ) AnnotationAssertion(rdfs:label obo:RO_0018029 "is antagonist of") AnnotationAssertion(rdfs:seeAlso obo:RO_0018029 ) SubObjectPropertyOf(obo:RO_0018029 obo:RO_0002449) @@ -6723,7 +6651,7 @@ SubObjectPropertyOf(obo:RO_0019002 obo:RO_0019000) # Object Property: obo:RO_0019501 (confers susceptibility to condition) AnnotationAssertion(obo:IAO_0000115 obo:RO_0019501 "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0019501 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0019501 ) AnnotationAssertion(rdfs:label obo:RO_0019501 "confers susceptibility to condition") SubObjectPropertyOf(obo:RO_0019501 obo:RO_0003304) @@ -6765,7 +6693,7 @@ SubObjectPropertyOf(obo:RO_HOM0000003 obo:RO_0002320) # Data Property: obo:RO_0002029 (has increased age-specific mortality rate) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24138933") Annotation(oboInOwl:hasDbXref "Wikipedia:Infant_mortality") obo:IAO_0000115 obo:RO_0002029 "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002029 ) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002029 "dos"^^xsd:string) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002029 "2018-05-22T16:43:28Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002029 "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.") AnnotationAssertion(rdfs:label obo:RO_0002029 "has increased age-specific mortality rate"@en) @@ -6777,16 +6705,16 @@ DataPropertyRange(obo:RO_0002029 DatatypeRestriction(xsd:short xsd:minInclusive # Classes ############################ -# Class: obo:BFO_0000002 (obo:BFO_0000002) +# Class: obo:BFO_0000002 (continuant) SubClassOf(obo:BFO_0000002 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000002)) SubClassOf(obo:BFO_0000002 ObjectAllValuesFrom(obo:RO_HOM0000000 obo:BFO_0000002)) -# Class: obo:BFO_0000003 (obo:BFO_0000003) +# Class: obo:BFO_0000003 (occurrent) SubClassOf(obo:BFO_0000003 ObjectAllValuesFrom(obo:RO_HOM0000000 obo:BFO_0000003)) -# Class: obo:BFO_0000015 (obo:BFO_0000015) +# Class: obo:BFO_0000015 (process) SubClassOf(obo:BFO_0000015 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000015)) @@ -6794,7 +6722,7 @@ SubClassOf(obo:BFO_0000015 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000015)) SubClassOf(obo:CHEBI_50906 obo:PATO_0000001) -# Class: obo:GO_0004842 (ubiquitin-protein transferase activity) +# Class: obo:GO_0004842 (ubiquitin-protein ligase activity) SubClassOf(obo:GO_0004842 ObjectHasSelf(obo:RO_0002482)) @@ -6802,7 +6730,7 @@ SubClassOf(obo:GO_0004842 ObjectHasSelf(obo:RO_0002482)) SubClassOf(obo:GO_0016301 ObjectHasSelf(obo:RO_0002481)) -# Class: obo:GO_0019107 (myristoyltransferase activity) +# Class: obo:GO_0019107 (obo:GO_0019107) SubClassOf(obo:GO_0019107 ObjectHasSelf(obo:RO_0018001)) @@ -6852,63 +6780,6 @@ AnnotationAssertion(rdfs:label obo:RO_0002577 "system") SubClassOf(obo:RO_0002577 obo:BFO_0000040) -############################ -# Named Individuals -############################ - -# Individual: obo:RO_0001901 (axiom holds for all times) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0001901 "## Elucidation - -This is used when the statement/axiom is assumed to hold true 'eternally' - -## How to interpret (informal) - -First the "atemporal" FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. - -## Example - - Class: nucleus - SubClassOf: part_of some cell - - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) - -## Notes - -This interpretation is *not* the same as an at-all-times relation") -AnnotationAssertion(rdfs:label obo:RO_0001901 "axiom holds for all times"@en) - -# Individual: obo:RO_0001902 (relation has no temporal argument) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0001902 "## Elucidation - -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. - -## Example: - - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm - - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y)") -AnnotationAssertion(rdfs:label obo:RO_0001902 "relation has no temporal argument"@en) - - SubClassOf(ObjectSomeValuesFrom(obo:RO_0002566 obo:BFO_0000040) ObjectUnionOf(ObjectSomeValuesFrom(obo:RO_0000056 ObjectSomeValuesFrom(obo:RO_0002418 obo:BFO_0000015)) ObjectSomeValuesFrom(obo:RO_0002215 ObjectSomeValuesFrom(obo:RO_0000056 ObjectSomeValuesFrom(obo:RO_0002418 obo:BFO_0000015))))) SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000050 obo:BFO_0000050) obo:RO_0002131) SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000050 obo:BFO_0000062) obo:BFO_0000062) @@ -7054,10 +6925,10 @@ SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0015001 obo:RO_0015003) obo:RO_00 SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(obo:BFO_0000066) obo:RO_0002234) obo:RO_0003000) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(obo:RO_0002176) obo:RO_0002176) obo:RO_0002170) DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002180 Variable() Variable()) ClassAtom(obo:BFO_0000015 Variable()) ClassAtom(obo:BFO_0000015 Variable()))Head(ObjectPropertyAtom(obo:RO_0002018 Variable() Variable()))) -DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ClassAtom(obo:GO_0003674 Variable()) ClassAtom(obo:GO_0003674 Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(swrla:isRuleEnabled "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(obo:RO_0002327 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ClassAtom(obo:GO_0003674 Variable()) ClassAtom(obo:GO_0003674 Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom(obo:GO_0003674 Variable()) ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()) ObjectPropertyAtom(obo:BFO_0000051 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()))) -DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom(obo:GO_0008150 Variable()) ObjectPropertyAtom(obo:BFO_0000050 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002331 Variable() Variable()))) +DLSafeRule(Annotation(swrla:isRuleEnabled "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(obo:GO_0008150 Variable()) ObjectPropertyAtom(obo:BFO_0000050 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002331 Variable() Variable()))) DLSafeRule(Annotation(rdfs:seeAlso ) Body(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ClassAtom(obo:GO_0016301 Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002447 Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002013 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002014 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable())))