diff --git a/apollo_sv-base.json b/apollo_sv-base.json index c755700..c0a469b 100644 --- a/apollo_sv-base.json +++ b/apollo_sv-base.json @@ -52,11 +52,14 @@ "val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)." }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2026-03-13" + "val" : "2026-07-19" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/apollo_sv-base.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2026-07-19/apollo_sv-base.json" }, "nodes" : [ { + "id" : "http://humanbehaviourchange.org/ontology/BCIO_036000", + "type" : "CLASS" + }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000000", "lbl" : "purely intentional entity", "type" : "CLASS", @@ -6490,7 +6493,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402", - "lbl" : "individual human behavior", + "lbl" : "obsolete individual human behavior", "type" : "CLASS", "meta" : { "definition" : { @@ -6506,9 +6509,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An individual behavior of a human being." }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "HumanBehavior" - } ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://humanbehaviourchange.org/ontology/BCIO_036000" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000403", @@ -11406,6 +11410,131 @@ "val" : "Intent to have one's child vaccinated." } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000653", + "lbl" : "human-to-human communicability", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A communicability among human beings (homo sapiens)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "communicability among human beings" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "The ability of a pathogen to transmit from one human host to another human host." + }, { + "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", + "val" : "HumanToHumanCommunicability" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000654", + "lbl" : "historical scenario", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disease scenario that represents or reconstructs an outbreak or epidemic that actually occurred, usually constrained by observed data." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "historical infectious disease scenario date" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "John Levander" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-04-04T19:36:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000655", + "lbl" : "hypothetical scenario", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disease scenario that represents a possible, assumed, projected, or counterfactual outbreak or epidemic, and does not need to correspond to a specific observed event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "hypothetical infecctious disease scenario" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "John Levander" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-04-04T19:52:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000656", + "lbl" : "antibody administration control strategy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ApolloDev/apollo-sv/issues/273" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Lucie Contamin" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-07-13T14:13:40Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000657", + "lbl" : "antibody administration census", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A population treatment census that is about one or more antibody administrations to organisms in a population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ApolloDev/apollo-sv/issues/273" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Lucie Contamin" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-07-13T13:52:47Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -11597,6 +11726,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/DRON_00000005", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/DRON_00000031", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/ENVO_01001079", "type" : "CLASS" @@ -11711,6 +11843,9 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020010", "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IDO_0000623", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/MF_0000073", "type" : "CLASS" @@ -12281,6 +12416,10 @@ "id" : "http://purl.obolibrary.org/obo/IAO_0000232", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000600", "type" : "PROPERTY", @@ -12317,6 +12456,14 @@ "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/created", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", "type" : "PROPERTY", @@ -12366,10 +12513,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000009", "pred" : "is_a", @@ -12494,10 +12637,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -12746,10 +12885,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000089", "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000025" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090", "pred" : "is_a", @@ -14105,7 +14240,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0007610" + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000403", "pred" : "is_a", @@ -14626,6 +14761,10 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000531", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532", + "pred" : "is_a", + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532", "pred" : "is_a", @@ -14685,7 +14824,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000546", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402" + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000547", "pred" : "is_a", @@ -14734,6 +14873,10 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000558", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000558", "pred" : "is_a", @@ -14933,7 +15076,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000601", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402" + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000602", "pred" : "is_a", @@ -15174,6 +15317,30 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000652", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000653", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IDO_0000623" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000654", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000184" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000655", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000184" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000656", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000194" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000657", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000187" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000657", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", + "obj" : "http://purl.obolibrary.org/obo/DRON_00000031" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "pred" : "is_a", @@ -15190,10 +15357,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -15252,7 +15415,7 @@ "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000009", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] @@ -15284,7 +15447,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032" @@ -15721,7 +15884,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0000100" diff --git a/apollo_sv-base.obo b/apollo_sv-base.obo index 53e58d7..74593a7 100644 --- a/apollo_sv-base.obo +++ b/apollo_sv-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: apollo_sv/releases/2026-03-13/apollo_sv-base.owl +data-version: apollo_sv/releases/2026-07-19/apollo_sv-base.owl idspace: ace_lexicon http://attempto.ifi.uzh.ch/ace_lexicon# idspace: dc http://purl.org/dc/elements/1.1/ idspace: doap http://usefulinc.com/ns/doap# @@ -21,7 +21,7 @@ property_value: dc:contributor "Shawn T. Brown" xsd:string property_value: dc:contributor "William R. Hogan" xsd:string property_value: dc:creator "Mathias Brochhausen" xsd:string property_value: dc:type IAO:8000001 -property_value: owl:versionInfo "2026-03-13" xsd:string +property_value: owl:versionInfo "2026-07-19" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-9881-1017" xsd:anyURI property_value: terms:description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string @@ -99,7 +99,6 @@ id: APOLLO_SV:00000008 name: software development def: "A planned process that has specified output a software product and that involves the creation of source code." [] is_a: COB:0000035 -is_a: OBI:0000011 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Software_development" xsd:string @@ -304,8 +303,7 @@ id: APOLLO_SV:00000033 name: counting def: "The planned process of finding the number of elements in a finite set of objects." [] is_a: COB:0000035 -is_a: OBI:0000011 -intersection_of: OBI:0000011 +intersection_of: COB:0000035 intersection_of: OBI:0000299 APOLLO_SV:00000032 ! count relationship: OBI:0000299 APOLLO_SV:00000032 ! count property_value: IAO:0000117 "Mathias Brochhausen" xsd:string @@ -747,7 +745,6 @@ property_value: IAO:0000600 "A vaccination efficacy that results from a vaccinat id: APOLLO_SV:00000090 name: vaccination efficacy study design execution def: "A study design execution that has as its specified output one or more measured vaccination efficacy data items" [] -is_a: COB:0000035 is_a: OBI:0000471 intersection_of: OBI:0000471 intersection_of: BFO:0000051 APOLLO_SV:00000142 ! vaccination @@ -3439,13 +3436,14 @@ property_value: IAO:0000600 "An individual behavior of a mosquito (organism of f [Term] id: APOLLO_SV:00000402 -name: individual human behavior +name: obsolete individual human behavior def: "An individual behavior of a human being." [] -is_a: GO:0007610 -property_value: APOLLO_SV:0000040 "HumanBehavior" xsd:string +is_a: oboInOwl:ObsoleteClass property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An individual behavior of a human being." xsd:string +is_obsolete: true +replaced_by: BCIO:036000 [Term] id: APOLLO_SV:00000403 @@ -4706,6 +4704,7 @@ id: APOLLO_SV:00000532 name: human travel def: "A geographical migration of an organism belonging to the species Homo sapiens." [] is_a: APOLLO_SV:00000480 ! geographical movement of organism +is_a: BCIO:036000 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4828,7 +4827,7 @@ property_value: IAO:0000600 "A planned process that is the realization of a dise id: APOLLO_SV:00000546 name: self-initiated travel avoidance behavior def: "Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition." [] -is_a: APOLLO_SV:00000402 ! individual human behavior +is_a: BCIO:036000 property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition." xsd:string @@ -4940,6 +4939,7 @@ property_value: IAO:0000118 "infectious disease forecasting software application id: APOLLO_SV:00000558 name: case series def: "An investigation that realizes the concretization of some disease state design and that has as an occurrent part some population survey that\nhas specified input some case definition." [] +is_a: OBI:0000011 is_a: OBI:0000066 property_value: APOLLO_SV:0000040 "CaseSeries" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -5347,7 +5347,7 @@ property_value: IAO:0000118 "hospitalization dataset" xsd:string id: APOLLO_SV:00000601 name: human daily movement def: "An individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time." [] -is_a: APOLLO_SV:00000402 ! individual human behavior +is_a: BCIO:036000 property_value: dc:creator http://orcid.org/0000-0002-9881-1017 property_value: dc:date "2021-03-16T16:29:53Z" xsd:dateTime property_value: IAO:0000111 "human daily movement behavior" xsd:string @@ -5824,6 +5824,62 @@ is_a: APOLLO_SV:00000650 ! intent to have a ward vaccinated property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Intent to have one's child vaccinated." xsd:string +[Term] +id: APOLLO_SV:00000653 +name: human-to-human communicability +def: "A communicability among human beings (homo sapiens)." [] +is_a: IDO:0000623 +property_value: APOLLO_SV:0000040 "HumanToHumanCommunicability" xsd:string +property_value: IAO:0000111 "communicability among human beings" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "The ability of a pathogen to transmit from one human host to another human host." xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 + +[Term] +id: APOLLO_SV:00000654 +name: historical scenario +def: "An infectious disease scenario that represents or reconstructs an outbreak or epidemic that actually occurred, usually constrained by observed data." [] +is_a: APOLLO_SV:00000184 ! infectious disease scenario +property_value: dc:contributor "John Levander" xsd:string +property_value: IAO:0000111 "historical infectious disease scenario date" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 +property_value: terms:created "2026-04-04T19:36:00Z" xsd:dateTime + +[Term] +id: APOLLO_SV:00000655 +name: hypothetical scenario +def: "An infectious disease scenario that represents a possible, assumed, projected, or counterfactual outbreak or epidemic, and does not need to correspond to a specific observed event." [] +is_a: APOLLO_SV:00000184 ! infectious disease scenario +property_value: dc:contributor "John Levander" xsd:string +property_value: IAO:0000111 "hypothetical infecctious disease scenario" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 +property_value: terms:created "2026-04-04T19:52:04Z" xsd:dateTime + +[Term] +id: APOLLO_SV:00000656 +name: antibody administration control strategy +def: "An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process." [] +is_a: APOLLO_SV:00000194 ! individual treatment control strategy +property_value: dc:contributor "Lucie Contamin" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000233 https://github.com/ApolloDev/apollo-sv/issues/273 +property_value: terms:created "2026-07-13T14:13:40Z" xsd:dateTime +property_value: terms:creator https://orcid.org/0000-0002-9881-1017 + +[Term] +id: APOLLO_SV:00000657 +name: antibody administration census +def: "A population treatment census that is about one or more antibody administrations to organisms in a population." [] +is_a: APOLLO_SV:00000187 ! population treatment census +relationship: IAO:0000136 DRON:00000031 +property_value: dc:contributor "Lucie Contamin" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000233 https://github.com/ApolloDev/apollo-sv/issues/273 +property_value: terms:created "2026-07-13T13:52:47Z" xsd:dateTime +property_value: terms:creator https://orcid.org/0000-0002-9881-1017 + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification @@ -5850,8 +5906,7 @@ id: APOLLO_SV:00000796 name: dataset creating def: "A planned process that has a data set as its specified output." [] is_a: COB:0000035 -is_a: OBI:0000011 -intersection_of: OBI:0000011 +intersection_of: COB:0000035 intersection_of: OBI:0000299 IAO:0000100 relationship: OBI:0000299 IAO:0000100 property_value: IAO:0000111 "creating a data set" xsd:string diff --git a/apollo_sv-base.owl b/apollo_sv-base.owl index 42962ec..5382a37 100644 --- a/apollo_sv-base.owl +++ b/apollo_sv-base.owl @@ -25,7 +25,7 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -42,7 +42,7 @@ C87985BA-6A8A-483A-A6B6-63975101F672 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). - 2026-03-13 + 2026-07-19 @@ -191,6 +191,12 @@ For the 1982-10-17 date, we suggest the dc:created annotation. + + + + + + @@ -245,6 +251,18 @@ For the 1982-10-17 date, we suggest the dc:created annotation. + + + + + + + + + + + + @@ -686,6 +704,12 @@ For example, the disposition of a piece of glass to bend light and the lattice s + + + + + + @@ -866,7 +890,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire - + @@ -882,7 +906,6 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire - @@ -1488,7 +1511,7 @@ can't recall whether we should use process or processual_entity for future - + @@ -1497,7 +1520,6 @@ can't recall whether we should use process or processual_entity for future - @@ -2768,7 +2790,6 @@ The time step value and unit are specified using a scalar value specification. - @@ -10046,13 +10067,14 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + An individual behavior of a human being. Matthew Diller William R. Hogan An individual behavior of a human being. - HumanBehavior - individual human behavior + + obsolete individual human behavior + true @@ -11916,6 +11938,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s + A geographical migration of an organism belonging to the species Homo sapiens. Matthew Diller @@ -12096,7 +12119,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition. Matthew Diller William R. Hogan @@ -12291,6 +12314,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s + @@ -13115,7 +13139,7 @@ has specified input some case definition. - + human daily movement behavior An individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time. William R. Hogan @@ -14071,6 +14095,111 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + + + + + + + + + + + + + + + + + + + + + + + + communicability among human beings + A communicability among human beings (homo sapiens). + William R. Hogan + The ability of a pathogen to transmit from one human host to another human host. + HumanToHumanCommunicability + + human-to-human communicability + + + + + + + + + historical infectious disease scenario date + An infectious disease scenario that represents or reconstructs an outbreak or epidemic that actually occurred, usually constrained by observed data. + William R. Hogan + John Levander + + 2026-04-04T19:36:00Z + historical scenario + + + + + + + + + hypothetical infecctious disease scenario + An infectious disease scenario that represents a possible, assumed, projected, or counterfactual outbreak or epidemic, and does not need to correspond to a specific observed event. + William R. Hogan + John Levander + + 2026-04-04T19:52:04Z + hypothetical scenario + + + + + + + + + An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process. + William R. Hogan + + Lucie Contamin + 2026-07-13T14:13:40Z + + antibody administration control strategy + + + + + + + + + + + + + + + A population treatment census that is about one or more antibody administrations to organisms in a population. + William R. Hogan + + Lucie Contamin + 2026-07-13T13:52:47Z + + antibody administration census + + + + @@ -14110,7 +14239,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si - + @@ -14119,7 +14248,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si - @@ -14333,6 +14461,12 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + @@ -14561,6 +14695,12 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + diff --git a/apollo_sv-full.json b/apollo_sv-full.json index 209d467..b57cd57 100644 --- a/apollo_sv-full.json +++ b/apollo_sv-full.json @@ -49,11 +49,70 @@ "val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)." }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2026-03-13" + "val" : "2026-07-19" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/apollo_sv-full.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2026-07-19/apollo_sv-full.json" }, "nodes" : [ { + "id" : "http://humanbehaviourchange.org/ontology/BCIO_006158", + "lbl" : "habitual behaviour", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An that results from a learnt stimulus-behaviour co-occurrence." + }, + "comments" : [ "A learnt stimulus-behaviour co-occurrence can lead to activation or execution of a habitual behaviour.\n\nHabitual behaviour can be an MoA or outcome depending on how 'habitual behaviour' is described in an intervention. The Behaviour Change-Intervention Ontology includes the class 'outcome behaviour' (definition: Human behavior that is an intervention outcome.), which would not be an MoA. When an intervention targets a habitual behaviour to achieve an outcome behaviour, the former qualifies as an MoA." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " \"Habit\" in the Theory of Interpersonal Behavior" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "\"Habits\" in the Motivation-Opportunities-Abilities" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "Published" + } ] + } + }, { + "id" : "http://humanbehaviourchange.org/ontology/BCIO_026022", + "lbl" : "educational facility", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A facility in which formal education is provided to a student population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "Published" + } ] + } + }, { + "id" : "http://humanbehaviourchange.org/ontology/BCIO_036000", + "lbl" : "individual human behaviour", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A bodily process of a human that involves co-ordinated contraction of striated muscles controlled by the brain." + }, + "comments" : [ " it is concerned with moving skeletal parts to which it is usually attached.' (https://www.collinsdictionary.com/dictionary/english/striped-muscle)", "The class human behaviour [BCIO:042000] has been made obsolete. If you want to refer to the behaviour of an individual, refer to individual human behaviour . If you want to refer to the behaviour of a group, refer to population behaviour.\n\nStriated muscles referred to in the definition do not ordinarily involve cardiac muscles.\n\nBehaviours are usually in response to an internal or external stimuli.\n\nEvery behaviour is associated with mental processes, but not every mental process is associated with behaviour. For instance, a verbal communication behaviour will involve mental processes to produce speech. However, mental processes associated with listening can occur without a person performing a behaviour.\n\n'behaviours' can involve a series of activities (e.g., more granular behaviours).\n\n'A 'striated muscle' can defined as 'a type of contractile tissue that is marked by transverse striations" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Also referred to in definitions as human behaviour or just behaviour." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "walks for 15 mins/day, never eats meat, attends school daily" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "Published" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "human behaviour" + }, { + "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", + "val" : "HumanBehavior" + } ] + } + }, { "id" : "http://purl.obolibrary.obo/obo/NCBITaxon_7160", "lbl" : "Aedes albopictus", "type" : "CLASS", @@ -6500,7 +6559,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402", - "lbl" : "individual human behavior", + "lbl" : "obsolete individual human behavior", "type" : "CLASS", "meta" : { "definition" : { @@ -6516,9 +6575,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An individual behavior of a human being." }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "HumanBehavior" - } ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://humanbehaviourchange.org/ontology/BCIO_036000" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000403", @@ -11416,6 +11476,131 @@ "val" : "Intent to have one's child vaccinated." } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000653", + "lbl" : "human-to-human communicability", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A communicability among human beings (homo sapiens)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "communicability among human beings" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "The ability of a pathogen to transmit from one human host to another human host." + }, { + "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", + "val" : "HumanToHumanCommunicability" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000654", + "lbl" : "historical scenario", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disease scenario that represents or reconstructs an outbreak or epidemic that actually occurred, usually constrained by observed data." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "historical infectious disease scenario date" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "John Levander" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-04-04T19:36:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000655", + "lbl" : "hypothetical scenario", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disease scenario that represents a possible, assumed, projected, or counterfactual outbreak or epidemic, and does not need to correspond to a specific observed event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "hypothetical infecctious disease scenario" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "John Levander" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-04-04T19:52:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000656", + "lbl" : "antibody administration control strategy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ApolloDev/apollo-sv/issues/273" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Lucie Contamin" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-07-13T14:13:40Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000657", + "lbl" : "antibody administration census", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A population treatment census that is about one or more antibody administrations to organisms in a population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ApolloDev/apollo-sv/issues/273" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Lucie Contamin" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-07-13T13:52:47Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -11575,10 +11760,28 @@ "val" : "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" + "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000004" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" + } ] + } + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/001-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11603,31 +11806,85 @@ "val" : "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" + "val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000007" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" + "val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/008-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" + "val" : "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/126-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" + "val" : "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/009-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" + "val" : "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/011-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " + "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/009-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " + "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/126-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " + "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/008-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " + "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/011-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11655,25 +11912,70 @@ "val" : "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." + "val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000006" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." + "val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000012" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" + "val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/077-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" + "val" : "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/108-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" + "val" : "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/079-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " + "val" : "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/108-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " + "val" : "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/079-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11685,7 +11987,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/017-002" + } ] + } }, "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ], "basicPropertyValues" : [ { @@ -11726,19 +12034,49 @@ "val" : "the interior of your mouth" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" + "val" : "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/134-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" + "val" : "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/018-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " + "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/134-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " + "val" : "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/018-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " + "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/017-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11760,19 +12098,52 @@ "val" : "BFO 2 Reference: Spatial regions do not participate in processes." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." + "val" : "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000002" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" + "val" : "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/035-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" + "val" : "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/036-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " + "val" : "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/036-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " + "val" : "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/035-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11791,25 +12162,70 @@ "val" : "TemporalRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional" + "val" : "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000003" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])" + "val" : "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/100-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" + "val" : "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/101-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" + "val" : "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/119-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " + "val" : "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/119-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " + "val" : "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/101-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " + "val" : "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/100-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11834,10 +12250,22 @@ "val" : "the surface of a sphere-shaped part of space" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" + "val" : "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/039-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " + "val" : "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/039-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11865,37 +12293,97 @@ "val" : "the spatiotemporal region occupied by the development of a cancer tumor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" + "val" : "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/095-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" + "val" : "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/096-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" + "val" : "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/099-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" + "val" : "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/098-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every spatiotemporal region occupies_spatiotemporal_region itself." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" + "val" : "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/107-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " + "val" : "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/107-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " + "val" : "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/099-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " + "val" : "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/096-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " + "val" : "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/095-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " + "val" : "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/098-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11907,7 +12395,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/083-003" + } ] + } }, "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ], "basicPropertyValues" : [ { @@ -11942,7 +12436,13 @@ "val" : "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " + "val" : "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/083-003" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11976,16 +12476,40 @@ "val" : "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/062-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" + "val" : "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/063-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " + "val" : "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/063-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " + "val" : "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/062-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12022,16 +12546,40 @@ "val" : "the role of this boundary to delineate where Utah and Colorado meet" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + "val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/058-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" + "val" : "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/060-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " + "val" : "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/060-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " + "val" : "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/058-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12050,10 +12598,22 @@ "val" : "ZeroDimensionalSpatialRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" + "val" : "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/037-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " + "val" : "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/037-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12090,16 +12650,40 @@ "val" : "the shape of your nostril" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" + "val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/055-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" + "val" : "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/105-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " + "val" : "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/055-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " + "val" : "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/105-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12111,7 +12695,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" + "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/050-003" + } ] + } }, "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ], "basicPropertyValues" : [ { @@ -12155,10 +12745,25 @@ "val" : "the smell of this portion of mozzarella" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." + "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " + "val" : "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/050-003" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12204,10 +12809,22 @@ "val" : "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" + "val" : "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/061-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " + "val" : "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/061-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12253,10 +12870,22 @@ "val" : "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])" + "val" : "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/027-004" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] " + "val" : "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/027-004" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12278,10 +12907,22 @@ "val" : "an edge of a cube-shaped portion of space." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])" + "val" : "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/038-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " + "val" : "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/038-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12340,25 +12981,46 @@ "val" : "your collection of Meissen ceramic plates." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " + "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000301" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." + "val" : "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000300" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" + "val" : "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/025-004" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " + "val" : "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/025-004" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12383,10 +13045,22 @@ "val" : "a sphere-shaped region of space," }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" + "val" : "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/040-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " + "val" : "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/040-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12450,10 +13124,22 @@ "val" : "your left nostril (a fiat part – the opening – of your left nasal cavity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" + "val" : "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/034-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " + "val" : "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/034-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12520,7 +13206,13 @@ "val" : "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" + "val" : "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/024-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12532,7 +13224,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" + "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/074-001" + } ] + } }, "comments" : [ "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." ], "basicPropertyValues" : [ { @@ -12552,7 +13250,13 @@ "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " + "val" : "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/074-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12583,10 +13287,22 @@ "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" + "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/064-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " + "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/064-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12598,7 +13314,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])" + "val" : "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/084-001" + } ] + } }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", @@ -12611,13 +13333,31 @@ "val" : "the boundary between the 2nd and 3rd year of your life." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" + "val" : "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/085-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " + "val" : "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/085-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " + "val" : "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/084-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12642,10 +13382,22 @@ "val" : "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" + "val" : "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/103-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " + "val" : "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/103-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", "val" : "Interval" @@ -12718,22 +13470,58 @@ "val" : "Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" + "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/019-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" + "val" : "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/020-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" + "val" : "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/021-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " + "val" : "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/019-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " + "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/021-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " + "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/020-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12745,7 +13533,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])" + "val" : "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/029-001" + } ] + } }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", @@ -12761,13 +13555,25 @@ "val" : "BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions." + "val" : "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000008" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every continuant fiat boundary is located at some spatial region at every time at which it exists" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] " + "val" : "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/029-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12820,10 +13626,22 @@ "val" : "the median sulcus of your tongue" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])" + "val" : "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/032-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " + "val" : "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/032-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12835,7 +13653,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])" + "val" : "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/093-002" + } ] + } }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", @@ -12854,13 +13678,31 @@ "val" : "The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])" + "val" : "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/094-005" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] " + "val" : "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/094-005" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " + "val" : "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/093-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12872,7 +13714,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])" + "val" : "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/057-001" + } ] + } }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", @@ -12888,7 +13736,13 @@ "val" : "a marriage bond, an instance of requited love, an obligation between one person and another." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] " + "val" : "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/057-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12907,10 +13761,22 @@ "val" : "TwoDimensionalContinuantFiatBoundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])" + "val" : "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/033-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " + "val" : "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/033-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12938,13 +13804,37 @@ "val" : "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])" + "val" : "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000001" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "requested by Melanie Courtot" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://groups.google.com/d/msg/bfo-owl-devel/s9Uug5QmAws/ZDRnpiIi_TUJ" + } ] + } + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/031-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " + "val" : "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/031-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12981,10 +13871,22 @@ "val" : "temporal instant." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" + "val" : "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/102-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " + "val" : "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/102-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -13006,7 +13908,13 @@ "val" : "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])" + "val" : "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/138-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -13038,7 +13946,32 @@ }, { "id" : "http://purl.obolibrary.org/obo/COB_0000035", "lbl" : "completely executed planned process", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "completely executed planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/cob.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0000082", + "lbl" : "planned process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/cob.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/DOID_0060478", "lbl" : "Zika fever", @@ -13262,6 +14195,25 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William Hogan" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/DRON_00000031", + "lbl" : "drug administration", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "administration of a drug product to an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" } ] } }, { @@ -13282,6 +14234,9 @@ }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-5039-2052" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "http://orcid.org/0000-0002-9881-1017" } ] } }, { @@ -13616,53 +14571,6 @@ "val" : "pub_type" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000001", - "lbl" : "geopolitical entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii)" - }, - "comments" : [ "In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000002", - "lbl" : "obsolete group of governmental organizations", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on." - }, - "comments" : [ "taken over by GEO_0000000401" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "obsolete aggregate of governmental organizations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000003", - "lbl" : "nation", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A geopolitical entity that is self contained and recognizes no higher political authority than itself." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000004", "lbl" : "subnational entity", @@ -13716,80 +14624,6 @@ "val" : "William R. Hogan" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000007", - "lbl" : "group of major administrative subdivisions", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common." - }, - "comments" : [ "Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000008", - "lbl" : "group of dependencies", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." - }, - "comments" : [ "Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000334", - "lbl" : "subcontinental land mass", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000335", - "lbl" : "contiguous land mass", - "type" : "CLASS", - "meta" : { - "comments" : [ "per the definition of 'contiguous' of \"being in actual contact : touching along a boundary or at a point\", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island.\n\nAt some point, we need an 'adjacent to' relation if BFO doesn't provide it.\n\nOne question is whether this class encompasses fiat parts of islands." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contiguous continental land mass" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000337", - "lbl" : "aggregate of governmental organizations", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members.\n" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000357", - "lbl" : "contiguous island land mass", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A subcontinental land mass that is part of an island and includes part of the land surface of the island." - }, - "comments" : [ "It cannot be a part of the island, for example, that is below water." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000369", - "lbl" : "aggregate of contiguous land masses", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000370", "lbl" : "geographical entity", @@ -13856,39 +14690,6 @@ "val" : "Location" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000373", - "lbl" : "body of water", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000374", - "lbl" : "continent", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000375", - "lbl" : "land mass", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000376", - "lbl" : "island", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000377", - "lbl" : "aggregate of geographical entities", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An object aggregate of geographical entities" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000378", - "lbl" : "aggregate of geographical features", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000390", - "lbl" : "aggregate of islands", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000391", "lbl" : "geopoli organization", @@ -13999,98 +14800,6 @@ "val" : "Amanda Hicks" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000401", - "lbl" : "aggregate of geopolitical organizations", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000402", - "lbl" : "obsolete aggregate of dependencies", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." - }, - "comments" : [ "Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000403", - "lbl" : "obsolete aggregate of major administrative subdivisions", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common" - }, - "comments" : [ "Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000404", - "lbl" : "aggregate of sovereign states", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common" - }, - "comments" : [ "examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000787", - "lbl" : "geodetic coordinate measurement datum", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum." - }, - "comments" : [ "latitude and longitude are key subtypes" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geodetic coordinate measurement datum" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Josh Hanna" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000788", "lbl" : "geodetic datum", @@ -14114,16 +14823,6 @@ "val" : "Wikipedia: https://en.wikipedia.org/wiki/Geodetic_datum\n\nDate accessed: 2015-04-13" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000789", - "lbl" : "plane angle measurement unit label", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "planar angular measurement unit label" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000797", "lbl" : "de jure sovereign state", @@ -14250,6 +14949,9 @@ "val" : "Wikipedia:Biological_process" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/24968" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" }, { @@ -14295,7 +14997,13 @@ "val" : "virulence" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-162906" + "val" : "Reactome:R-HSA-162906", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "HIV Infection" + } ] + } }, { "val" : "Wikipedia:Viral_life_cycle" } ], @@ -14322,9 +15030,21 @@ "val" : "phosphokinase activity" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-6788855" + "val" : "Reactome:R-HSA-6788855", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "FN3KRP phosphorylates PsiAm, RibAm" + } ] + } }, { - "val" : "Reactome:R-HSA-6788867" + "val" : "Reactome:R-HSA-6788867", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "FN3K phosphorylates ketosamines" + } ] + } } ] } }, { @@ -14354,11 +15074,29 @@ "xrefs" : [ "GOC:bf", "GOC:jl" ] } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-162588" + "val" : "Reactome:R-HSA-162588", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Budding and maturation of HIV virion" + } ] + } }, { - "val" : "Reactome:R-HSA-168255" + "val" : "Reactome:R-HSA-168255", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Influenza Infection" + } ] + } }, { - "val" : "Reactome:R-HSA-9609646" + "val" : "Reactome:R-HSA-9609646", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "HCMV Infection" + } ] + } } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", @@ -14394,6 +15132,9 @@ "val" : "single-organism reproductive behavior" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/23491" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" }, { @@ -14431,6 +15172,9 @@ "val" : "Wikipedia:Sexual_reproduction" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22929" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -14453,6 +15197,9 @@ "val" : "Wikipedia:Asexual_reproduction" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22929" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -14475,6 +15222,9 @@ "val" : "Wikipedia:Reproduction" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27054" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" }, { @@ -14513,6 +15263,9 @@ "val" : "single-multicellular organism process" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27189" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" }, { @@ -14570,7 +15323,22 @@ "pred" : "hasRelatedSynonym", "val" : "symbiotic process" } ], + "xrefs" : [ { + "val" : "Reactome:R-HSA-9839923", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Dengue Virus Infection" + } ] + } + } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/14807" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/20191" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0043298" }, { @@ -14667,9 +15435,18 @@ "val" : "other organism invasion" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-173107" + "val" : "Reactome:R-HSA-173107", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Binding and entry of HIV virion" + } ] + } } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/18563" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" }, { @@ -14725,9 +15502,18 @@ "val" : "interspecies interaction with other organisms" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-9824443" + "val" : "Reactome:R-HSA-9824443", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Parasitic Infection Pathways" + } ] + } } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/20191" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -14750,9 +15536,18 @@ "val" : "reproductive process in a multicellular organism" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-1474165" + "val" : "Reactome:R-HSA-1474165", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Reproduction" + } ] + } } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27054" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -14799,11 +15594,34 @@ "val" : "growth of symbiont in host vacuole" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-9635486" + "val" : "Reactome:R-HSA-9635486", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Infection with Mycobacterium tuberculosis" + } ] + } }, { - "val" : "Reactome:R-HSA-9658195" + "val" : "Reactome:R-HSA-9640148", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Infection with Enterobacteria" + } ] + } + }, { + "val" : "Reactome:R-HSA-9658195", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Leishmania infection" + } ] + } } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/20191" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0044112" }, { @@ -14881,9 +15699,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of measurement unit labels are liters, inches, weight per volume." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -14899,9 +15714,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -15026,17 +15838,11 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An information content entity that is part of some data item and is used to partially define the denotation of that data item." + "val" : "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data item label" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "datum label" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" @@ -15046,15 +15852,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP: IAO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "datum label" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. \n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -15310,9 +16110,12 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." + "val" : "An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data entity" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data item" }, { @@ -15348,6 +16151,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "data item" } ] } }, { @@ -15465,12 +16271,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." + "val" : "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "scalar measurement datum" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "10 feet. 3 ml." }, { @@ -15488,9 +16291,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -16134,11 +16934,14 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000187" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/172" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000100", - "lbl" : "data set", + "lbl" : "homogenous data collection", "type" : "CLASS", "meta" : { "definition" : { @@ -16146,7 +16949,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data set" + "val" : "homogenous data collection" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." @@ -16166,8 +16969,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000042" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "data set" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" @@ -16328,9 +17131,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -19661,6 +20461,25 @@ "val" : "https://en.wikipedia.org/wiki/Extract,_transform,_load" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000651", + "lbl" : "title section", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "the section of the document where the title appears" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Charles Tapley Hoyt" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/286" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000701", "lbl" : "descriptive data section", @@ -19933,6 +20752,31 @@ "val" : "https://github.com/information-artifact-ontology/IAO/issues/259" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0001000", + "lbl" : "data collection", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A data entity that consists of multiple data entities." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data collection" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Sebastian Duesing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "data set" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/283" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obi-ontology/obi/issues/1877" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020000", "lbl" : "identifier", @@ -32005,74 +32849,6 @@ "val" : "NIAID GSCID-BRC" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001620", - "lbl" : "latitude coordinate measurement datum", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A measurement datum that is the measure of the latitude coordinate of a site." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "latitude coordinate measurement datum" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Chris Stoeckert, Jie Zheng" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "latitude" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "NIAID GSCID-BRC metadata working group" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/OBI_0001886", - "val" : "Specimen Collection Location - Latitude" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "NIAID GSCID-BRC" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001621", - "lbl" : "longitude coordinate measurement datum", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A measurement datum that is the measure of the longitude coordinate of a site." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "longitude coordinate measurement datum" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Chris Stoeckert, Jie Zheng" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "longitude" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "NIAID GSCID-BRC metadata working group" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/OBI_0001886", - "val" : "Specimen Collection Location - Longitude" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "NIAID GSCID-BRC" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001628", "lbl" : "investigation identifier", @@ -32140,54 +32916,10 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001931", - "lbl" : "scalar value specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A value specification that consists of two parts: a numeral and a unit label" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "scalar value specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001933", - "lbl" : "value specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An information content entity that specifies a value within a classification scheme or on a quantitative scale." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "value specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001958", "lbl" : "systematic review study design", @@ -32275,7 +33007,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A planned process that produces output data from input data." + "val" : "A data transformation is a process which produces output data from input data" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -32745,8 +33477,14 @@ }, "comments" : [ "From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.jbiomedsem.com/content/1/1/10" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "creation date: 2009-06-23T11:53:49Z" } ] } }, { @@ -33302,11 +34040,14 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A facility that is run by a school organization and is the bearer of a school function." + "val" : "An educational facility that is run by a school organization and is the bearer of a school function." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" } ] } }, { @@ -33455,21 +34196,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000117", - "lbl" : "size", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim", "http://purl.obolibrary.org/obo/pato#scalar_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000122", "lbl" : "length", @@ -33674,24 +34401,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001323", - "lbl" : "area", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent." - }, - "comments" : [ "MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area." ], - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim", "http://purl.obolibrary.org/obo/pato#mpath_slim", "http://purl.obolibrary.org/obo/pato#scalar_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001708", "lbl" : "1-D extent", @@ -33713,27 +34422,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001709", - "lbl" : "2-D extent", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "2-D size" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001961", "lbl" : "in contact with", @@ -34228,7 +34916,7 @@ "val" : "End of the life of an organism.", "xrefs" : [ "XAO:0000437" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "death" @@ -34248,7 +34936,7 @@ "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "developmental stage" @@ -34619,7 +35307,7 @@ "val" : "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ] } }, { "id" : "http://purl.obolibrary.org/obo/UO_0000000", @@ -34639,6 +35327,9 @@ "lbl" : "length unit", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A unit which is a standard measure of the distance between two points." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "length unit" @@ -34652,6 +35343,9 @@ "lbl" : "mass unit", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A unit which is a standard measure of the amount of matter/energy of a physical object." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "mass unit" @@ -34665,6 +35359,9 @@ "lbl" : "time unit", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A unit which is a standard measure of the dimension in which events occur in sequence." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "time unit" @@ -34679,26 +35376,6 @@ "val" : "unitOfTime" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/UO_0000047", - "lbl" : "area unit", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A unit which is a standard measure of the amount of a 2-dimensional flat surface." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uo#unit_group_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/uo.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "george gkoutos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "unit.ontology" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/UO_0000186", "lbl" : "dimensionless unit", @@ -34953,17 +35630,6 @@ } ], "deprecated" : true } - }, { - "id" : "http://purl.obolibrary.org/obo/geo.owl/GEO_000000399", - "lbl" : "supranational entity", - "type" : "CLASS", - "meta" : { - "comments" : [ "e.g., the EU" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - } ] - } }, { "id" : "http://purl.org/obo/owl/FBcv#FBcv_0000209", "lbl" : "news article", @@ -34994,17 +35660,8 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", - "lbl" : "obsolete_class", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://www.geneontology.org/formats/oboInOwl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147487145" - } ] - } + "lbl" : "Obsolete Class", + "type" : "CLASS" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#Subset", "type" : "CLASS" @@ -35103,7 +35760,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -35447,53 +36104,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000083", - "lbl" : "occupies spatial region at some time", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "located-at-r_st" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "occupiesSpatialRegionAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: independent continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: spatial region" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { @@ -35505,60 +36115,12 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000110", "lbl" : "has continuant part at all times", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-has-part_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "hasContinuantPartAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000111", "lbl" : "has proper continuant part at all times", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-has-ppart_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "hasProperContinuantPartAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000113", "lbl" : "has material basis at all times", @@ -35690,32 +36252,6 @@ "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000123", - "lbl" : "has spatial occupant at some time", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "r-location-of_st" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000132", "lbl" : "part of occurrent", @@ -35809,33 +36345,8 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000137", - "lbl" : "proper part of continuant at all times", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001])" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-ppart-of_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "properContinuantPartOfAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000138", "lbl" : "proper part of occurrent", @@ -36083,93 +36594,8 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000177", - "lbl" : "part of continuant at all times", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-part-of_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "continuantPartOfAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mary’s arm continuant_part_of Mary in the time of her life prior to her operation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000181", "lbl" : "has proper temporal part", @@ -36198,93 +36624,37 @@ "type" : "PROPERTY", "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000187", - "lbl" : "has continuant part at all times that part exists", + "id" : "http://purl.obolibrary.org/obo/IAO_0000011", + "lbl" : "is directed towards", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)" + "val" : "A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality." }, + "comments" : [ "In the definition source, the relation is called 'is_about'. To avoid confusion with the existing \"is about\" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-has-part-object_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'." + "val" : "One of my mental representations is directed towards the Pacific Ocean." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person: William Hogan" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://ceur-ws.org/Vol-1515/regular10.pdf" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/285" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000328", - "lbl" : "is in aggregate", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000329", - "lbl" : "is subordinate authority of", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2." - }, - "comments" : [ "\n'is subordinate authority of'\nDomain: governing organization\nRange: governing organization\nFormal properties: transitive, anti-symmetric, irreflexive\nNatural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000336", - "lbl" : "has jurisdiction in", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "comments" : [ "It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c.\n\nin other words, it is perfectly fine to say:\na disjoint b\nc has_jurisdiction_in a\nc has_jurisdiction_in b\n\notherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it \"United States territory\", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities.", "a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories.", "if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b." ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000039", "lbl" : "has measurement unit label", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "A relation between a value specification and its unit of measurement." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has measurement unit label" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000135", "lbl" : "obsolete_specifically denotes", @@ -36325,7 +36695,7 @@ "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "is_about is a (currently) primitive relation that relates an information artifact to an entity." + "val" : "A (currently) primitive relation that relates an information artifact to an entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -36342,9 +36712,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { @@ -36662,19 +37029,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000293", - "lbl" : "has_specified_input", + "lbl" : "has specified input", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The inverse property of is_specified_input_of" + "val" : "The inverse property of is specified input of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has_specified_input" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has_specified_input" + "val" : "has specified input" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "see is_input_of example_of_usage" @@ -36699,55 +37063,25 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000295", - "lbl" : "is_specified_input_of", + "lbl" : "is specified input of", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is_specified_input_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000299", - "lbl" : "has_specified_output", + "lbl" : "has specified output", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The inverse property of is_specified_output_of" + "val" : "The inverse property of is specified output of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has specified output" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has_specified_output" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has_specified_output" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -36766,9 +37100,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -36780,22 +37111,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000312", - "lbl" : "is_specified_output_of", + "lbl" : "is specified output of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." + "val" : "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is specified output of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is_specified_output_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is_specified_output_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -36808,9 +37133,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -36844,30 +37166,8 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001938", - "lbl" : "has value specification", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "A relation between an information content entity and a value specification that specifies its value." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has value specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: James A. Overton" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", "lbl" : "owns", @@ -37027,9 +37327,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "participates_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -37062,9 +37359,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" @@ -38364,7 +38658,11 @@ "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." }, "comments" : [ "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" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002305", @@ -38375,7 +38673,11 @@ "definition" : { "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002314", @@ -40009,19 +40311,7 @@ "id" : "http://purl.obolibrary.org/obo/IAO_0000004", "lbl" : "has measurement value", "type" : "PROPERTY", - "propertyType" : "DATA", - "meta" : { - "definition" : { - "val" : "A relation between a scalar measurement data item and a number that quantifies it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The range should probably not be restricted to \"float\". It makes sense to set it to \"real\". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "propertyType" : "DATA" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000404", "lbl" : "has x coordinate value", @@ -40055,37 +40345,6 @@ "val" : "angular degree" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000791", - "lbl" : "radian", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A unit of measurement of planar angles where a full circle is 2π. Specifically the angle is the length of the arc subtended by the angle divided by the circumference of the circle." - }, - "comments" : [ "Technically in the S.I. system it is a derived unit m•m^-1." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "radian" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Josh Hanna" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000796", - "lbl" : "square mile", - "type" : "INDIVIDUAL", - "meta" : { - "comments" : [ "An area unit which is equal to the area enclosed by a square in a flat plane which is one mile on every side." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "square mile" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", @@ -40489,6 +40748,28 @@ "val" : "https://orcid.org/0000-0002-7356-1779" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0001002", + "lbl" : "domain entity does not exist", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0002-4142-7153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/136" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "https://orcid.org/0000-0002-4142-7153" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UO_0000034", "lbl" : "week", @@ -40497,11 +40778,17 @@ "comments" : [ "\"A time unit which is equal to 7 days.\" [Wikipedia:Wikipedia]" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UO_0000080", - "lbl" : "square meter", + "id" : "https://orcid.org/0000-0002-9881-1017", + "lbl" : "William R. Hogan", "type" : "INDIVIDUAL", "meta" : { - "comments" : [ "\"An area unit which is equal to an area enclosed by a square with sides each 1 meter long.\" [NIST:NIST]" ] + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-04-04T19:54:38Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] } }, { "id" : "http://protege.stanford.edu/plugins/owl/protege#defaultLanguage", @@ -40659,109 +40946,9 @@ "val" : "VIVO-ISF" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000009", - "lbl" : "US State Two Digit Identifier", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000010", - "lbl" : "US State Two Letter Abbreviation", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000011", - "lbl" : "US State Ens Identifier", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000021", - "lbl" : "UN Numerical Code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000022", - "lbl" : "ISO 3166-1-alpha-3 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000023", - "lbl" : "ISO 3166-1-alpha-2 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000358", - "lbl" : "Proposed Apollo Location Code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000359", - "lbl" : "ISO 3166-2 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035330", - "lbl" : "geonameid", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "integer id of record in geonames database" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonameid" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035331", - "lbl" : "admin1 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "fipscode (subject to change to iso code), see exceptions below, see file admin1Codes.txt for display names of this code; varchar(20)" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonames admin1 code" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035332", - "lbl" : "admin2 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "code for the second administrative division, a county in the US, see file admin2Codes.txt; varchar(80)" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonames admin2 code" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035333", - "lbl" : "admin3 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "code for third level administrative division, varchar(20)" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonames admin3 code" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035334", - "lbl" : "admin4 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "code for fourth level administrative division, varchar(20)" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonames admin4 code" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000111", - "lbl" : "editor preferred term~editor preferred label", + "lbl" : "editor preferred term", "type" : "PROPERTY", "propertyType" : "ANNOTATION", "meta" : { @@ -40975,6 +41162,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { @@ -41061,22 +41251,46 @@ "definition" : { "val" : "An IRI or similar locator for a request or discussion of an ontology term." }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term.", "The 'tracker item' can associate a tracker with a specific ontology term." ], + "xrefs" : [ { + "val" : "IAO:0000233" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term tracker item" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { @@ -41618,10 +41832,366 @@ "val" : "https://orcid.org/0000-0002-8688-6599" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0002001", + "lbl" : "preferred label for community", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A provenance property that denotes a synonym to be the preferred one for a specific community." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease \"A\" and another one \"B\" (but they are the same thing)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/185" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2025-06-02" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing abbreviations or initialisms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003001", + "lbl" : "ambiguous synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing ambiguous synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", + "lbl" : "dubious synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing dubious synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "lbl" : "layperson synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing layperson or colloquial synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing pluralization synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003005", + "lbl" : "UK spelling synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing UK spelling variants" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003006", + "lbl" : "misspelling", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for common misspellings" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/132" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003007", + "lbl" : "misnomer", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/133" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003008", + "lbl" : "previous name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for names that have been used as primary labels in the past." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/139" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-07-25" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003009", + "lbl" : "legal name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for the legal entity name" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/141" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-07-27" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003010", + "lbl" : "International Nonproprietary Name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "INN" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) \"paracetamol\". In some cases such as this one, the INN might be the same as the ontology's primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/149" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-09-30" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "lbl" : "latin term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing Latin term synonyms." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "nasopharynx (UBERON:0001728) has the latin name \"pars nasalis pharyngis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/146" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-1773-2692" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-10-12" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003012", + "lbl" : "acronym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/135" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-11-01" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003014", + "lbl" : "has ontology hierarchical property", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: ` a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/292" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2025-09-17" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0004000", + "lbl" : "has symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A serial number such as \"12324X\"; a stop sign; a written proper name such as \"OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/144" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6523-4866" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2024-03-25" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001900", "lbl" : "temporal interpretation", @@ -41795,18 +42365,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "lbl" : "eco subset", @@ -41848,10 +42406,6 @@ "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/uo#unit_group_slim", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/contributor", "type" : "PROPERTY", @@ -41945,6 +42499,14 @@ "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/created", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", "type" : "PROPERTY", @@ -42020,14 +42582,19 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-7356-1779" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2024-03-18" } ] } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "lbl" : "has_definition", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -42178,6 +42745,18 @@ } } ], "edges" : [ { + "sub" : "http://humanbehaviourchange.org/ontology/BCIO_006158", + "pred" : "is_a", + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" + }, { + "sub" : "http://humanbehaviourchange.org/ontology/BCIO_026022", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" + }, { + "sub" : "http://humanbehaviourchange.org/ontology/BCIO_036000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000060" + }, { "sub" : "http://purl.obolibrary.obo/obo/NCBITaxon_7160", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_53541" @@ -42209,10 +42788,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000009", "pred" : "is_a", @@ -42337,10 +42912,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -42589,10 +43160,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000089", "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000025" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090", "pred" : "is_a", @@ -43948,7 +44515,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0007610" + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000403", "pred" : "is_a", @@ -44469,6 +45036,10 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000531", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532", + "pred" : "is_a", + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532", "pred" : "is_a", @@ -44528,7 +45099,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000546", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402" + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000547", "pred" : "is_a", @@ -44577,6 +45148,10 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000558", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000558", "pred" : "is_a", @@ -44776,7 +45351,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000601", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402" + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000602", "pred" : "is_a", @@ -45017,6 +45592,30 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000652", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000653", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IDO_0000623" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000654", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000184" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000655", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000184" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000656", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000194" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000657", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000187" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000657", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", + "obj" : "http://purl.obolibrary.org/obo/DRON_00000031" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "pred" : "is_a", @@ -45033,10 +45632,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -45220,6 +45815,10 @@ }, { "sub" : "http://purl.obolibrary.org/obo/COB_0000035", "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/COB_0000082" + }, { + "sub" : "http://purl.obolibrary.org/obo/COB_0000082", + "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/DOID_0060478", @@ -45245,6 +45844,10 @@ "sub" : "http://purl.obolibrary.org/obo/DRON_00000005", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/DRON_00000074" + }, { + "sub" : "http://purl.obolibrary.org/obo/DRON_00000031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000090" }, { "sub" : "http://purl.obolibrary.org/obo/DRON_00000074", "pred" : "is_a", @@ -45313,26 +45916,10 @@ "sub" : "http://purl.obolibrary.org/obo/FBcv_0000787", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000001", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000003", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GEO_000000400" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000004", - "pred" : "http://purl.obolibrary.org/obo/GEO_000000329", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000396" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000005", "pred" : "is_a", @@ -45341,58 +45928,6 @@ "sub" : "http://purl.obolibrary.org/obo/GEO_000000006", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GEO_000000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000007", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000007", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000005" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000008", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000006" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000334", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000375" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000334", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000137", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000374" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000335", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000334" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000337", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000337", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000400" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000357", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000334" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000369", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000375" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000369", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000377" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000369", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000375" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000370", "pred" : "is_a", @@ -45405,46 +45940,6 @@ "sub" : "http://purl.obolibrary.org/obo/GEO_000000372", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GEO_000000370" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000373", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000372" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000374", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000375" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000375", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000372" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000376", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000334" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000377", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000377", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000370" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000378", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000377" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000378", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000371" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000390", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000369" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000390", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000376" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000391", "pred" : "is_a", @@ -45469,42 +45964,10 @@ "sub" : "http://purl.obolibrary.org/obo/GEO_000000400", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000401", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000401", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000391" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000402", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000403", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000404", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000404", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000396" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000787", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000109" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000788", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000789", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000797", "pred" : "is_a", @@ -45800,7 +46263,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000100", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" + "obj" : "http://purl.obolibrary.org/obo/IAO_0001000" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000101", "pred" : "is_a", @@ -46137,10 +46600,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000443", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000443", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000443", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46152,7 +46611,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000444", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000445", "pred" : "is_a", @@ -46161,10 +46620,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000572", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000572", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000572", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46181,10 +46636,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000574", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000574", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000574", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -46196,7 +46647,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000575", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000575", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46233,10 +46684,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000580", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000580", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000580", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46557,10 +47004,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000650", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000650", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000650", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46569,6 +47012,10 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000650", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0000651", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000314" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000701", "pred" : "is_a", @@ -46601,6 +47048,10 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000708", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000578" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0001000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020000", "pred" : "is_a", @@ -46621,10 +47072,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -49240,7 +49687,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000115", "pred" : "is_a", @@ -49260,7 +49707,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000471", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000576", "pred" : "is_a", @@ -49321,14 +49768,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0001615", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000300" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001620", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000787" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001621", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000787" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0001628", "pred" : "is_a", @@ -49337,14 +49776,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0001629", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001931", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0001933" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001933", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0001958", "pred" : "is_a", @@ -49636,7 +50067,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_026022" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", @@ -49721,18 +50152,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001241", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001323", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001709" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001708", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001709", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001961", "pred" : "is_a", @@ -49861,10 +50284,6 @@ "sub" : "http://purl.obolibrary.org/obo/UO_0000003", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/UO_0000047", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/UO_0000186", "pred" : "is_a", @@ -49905,10 +50324,6 @@ "sub" : "http://purl.obolibrary.org/obo/VO_0000590", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/geo.owl/GEO_000000399", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000400" }, { "sub" : "http://purl.org/obo/owl/FBcv#FBcv_0000209", "pred" : "is_a", @@ -49929,18 +50344,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000107" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000790", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000789" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000791", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000789" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000796", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/UO_0000047" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000002", "pred" : "type", @@ -50021,14 +50424,18 @@ "sub" : "http://purl.obolibrary.org/obo/OMO_0001000", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMO_0001002", + "pred" : "type", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/UO_0000034", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/UO_0000003" }, { - "sub" : "http://purl.obolibrary.org/obo/UO_0000080", + "sub" : "https://orcid.org/0000-0002-9881-1017", "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/UO_0000047" + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000004", "pred" : "subPropertyOf", @@ -50085,10 +50492,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000075", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000110", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000111", "pred" : "subPropertyOf", @@ -50121,10 +50524,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000136", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000139" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000137", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000177" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000138", "pred" : "subPropertyOf", @@ -50145,10 +50544,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000156", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000177", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000181", "pred" : "subPropertyOf", @@ -50161,10 +50556,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000184", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000066" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000187", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000039", "pred" : "subPropertyOf", @@ -50173,10 +50564,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000135", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000136", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000142", "pred" : "subPropertyOf", @@ -50229,10 +50616,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000293", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0000295", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000056" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000299", "pred" : "subPropertyOf", @@ -50249,10 +50632,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000417", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001938", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", "pred" : "subPropertyOf", @@ -50277,14 +50656,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000053", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0000056", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0000057", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000079", "pred" : "subPropertyOf", @@ -50949,22 +51320,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000066", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000067" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000075", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000328" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000083", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000123" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000117", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000132" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000137", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000142", "pred" : "inverseOf", @@ -50985,6 +51344,10 @@ "sub" : "http://purl.obolibrary.org/obo/OBIB_0000732", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/OBIB_0000735" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000293", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000295" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000299", "pred" : "inverseOf", @@ -51119,7 +51482,7 @@ "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000009", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] @@ -51151,7 +51514,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032" @@ -51588,7 +51951,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0000100" @@ -51600,16 +51963,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000798" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GEO_000000004", - "genusIds" : [ "http://purl.obolibrary.org/obo/GEO_000000400" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/GEO_000000329", - "fillerId" : "http://purl.obolibrary.org/obo/GEO_000000396" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GEO_000000787", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000109" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019098", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007610", "http://purl.obolibrary.org/obo/GO_0048609" ] @@ -51638,7 +51991,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020010", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020000" @@ -51792,7 +52145,7 @@ } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000312", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035", "http://purl.obolibrary.org/obo/OBI_0000011" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "allValuesFromEdges" : [ { "sub" : "http://purl.obolibrary.org/obo/IAO_0000013", "pred" : "http://purl.obolibrary.org/obo/OBI_0000312", @@ -51847,14 +52200,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000083", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000006" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000123", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000155", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -51871,14 +52216,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000185", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/GEO_000000329", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/GEO_000000400" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GEO_000000400" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/GEO_000000336", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/GEO_000000400" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GEO_000000375" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000136", "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ] @@ -51911,10 +52248,10 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000582" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000293", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000299", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035", "http://purl.obolibrary.org/obo/OBI_0000011" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], diff --git a/apollo_sv-full.obo b/apollo_sv-full.obo index 75acdd5..e730417 100644 --- a/apollo_sv-full.obo +++ b/apollo_sv-full.obo @@ -1,6 +1,5 @@ format-version: 1.2 -data-version: apollo_sv/releases/2026-03-13/apollo_sv-full.owl -subsetdef: attribute_slim "" +data-version: apollo_sv/releases/2026-07-19/apollo_sv-full.owl subsetdef: common_anatomy "" subsetdef: efo_slim "" subsetdef: gocheck_do_not_annotate "" @@ -24,16 +23,25 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" subsetdef: human_subset "" subsetdef: mouse_subset "" -subsetdef: mpath_slim "" subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" -subsetdef: scalar_slim "" subsetdef: uberon_slim "" -subsetdef: unit_group_slim "" subsetdef: upper_level "" subsetdef: vertebrate_core "" -synonymtypedef: OMO:0003004 "" +synonymtypedef: OMO:0003000 "abbreviation" +synonymtypedef: OMO:0003001 "ambiguous synonym" +synonymtypedef: OMO:0003002 "dubious synonym" +synonymtypedef: OMO:0003003 "layperson synonym" +synonymtypedef: OMO:0003004 "plural form" +synonymtypedef: OMO:0003005 "UK spelling synonym" +synonymtypedef: OMO:0003006 "misspelling" +synonymtypedef: OMO:0003007 "misnomer" +synonymtypedef: OMO:0003008 "previous name" +synonymtypedef: OMO:0003009 "legal name" +synonymtypedef: OMO:0003010 "International Nonproprietary Name" +synonymtypedef: OMO:0003011 "latin term" +synonymtypedef: OMO:0003012 "acronym" idspace: ace_lexicon http://attempto.ifi.uzh.ch/ace_lexicon# idspace: dc http://purl.org/dc/elements/1.1/ idspace: doap http://usefulinc.com/ns/doap# @@ -56,7 +64,7 @@ property_value: dc:contributor "Mike Wagner" xsd:string property_value: dc:contributor "Shawn T. Brown" xsd:string property_value: dc:contributor "William R. Hogan" xsd:string property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: owl:versionInfo "2026-03-13" xsd:string +property_value: owl:versionInfo "2026-07-19" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-9881-1017" xsd:anyURI property_value: terms:description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string @@ -134,7 +142,6 @@ id: APOLLO_SV:00000008 name: software development def: "A planned process that has specified output a software product and that involves the creation of source code." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Software_development" xsd:string @@ -327,7 +334,7 @@ id: APOLLO_SV:00000032 name: count def: "A measurement datum that is the output of counting." [] is_a: IAO:0000109 ! measurement datum -intersection_of: IAO:0000027 ! data item +intersection_of: IAO:0000027 ! data entity intersection_of: OBI:0000312 APOLLO_SV:00000033 ! is specified output of counting relationship: OBI:0000312 APOLLO_SV:00000033 ! is specified output of counting property_value: APOLLO_SV:0000040 "count" xsd:string @@ -339,8 +346,7 @@ id: APOLLO_SV:00000033 name: counting def: "The planned process of finding the number of elements in a finite set of objects." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -intersection_of: OBI:0000011 ! planned process +intersection_of: COB:0000035 ! completely executed planned process intersection_of: OBI:0000299 APOLLO_SV:00000032 ! has specified output count relationship: OBI:0000299 APOLLO_SV:00000032 ! has specified output count property_value: IAO:0000117 "Mathias Brochhausen" xsd:string @@ -599,7 +605,7 @@ def: "An action specification that specifies the length of the time steps interv comment: simulation time step value\nsimulation time step unit\nsimulation run length\n\nThe time step value and unit are specified using a scalar value specification. is_a: APOLLO_SV:00000793 ! epidemic simulator action specification relationship: IAO:0000136 APOLLO_SV:00000066 ! is about simulation of time step -relationship: OBI:0001938 OBI:0001931 ! has value specification scalar value specification +relationship: OBI:0001938 OBI:0001931 relationship: part_of APOLLO_SV:00000007 ! simulation software application property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "An action specification that specifies the length of the time steps interval assumed in a simulation." xsd:string @@ -738,7 +744,7 @@ property_value: IAO:0000600 "A control strategy dose schedule specifies the inte id: APOLLO_SV:00000085 name: age data in age brackets data set def: "A data set consisting of measurements of age organized in age brackets." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: IAO:0000111 "age structure data set" xsd:string property_value: IAO:0000600 "A data set consisting of measurements of age organized in age brackets." xsd:string @@ -782,7 +788,6 @@ property_value: IAO:0000600 "A vaccination efficacy that results from a vaccinat id: APOLLO_SV:00000090 name: vaccination efficacy study design execution def: "A study design execution that has as its specified output one or more measured vaccination efficacy data items" [] -is_a: COB:0000035 ! completely executed planned process is_a: OBI:0000471 ! study design execution intersection_of: OBI:0000471 ! study design execution intersection_of: has_part APOLLO_SV:00000142 ! vaccination @@ -1098,7 +1103,7 @@ property_value: IAO:0000600 "An event in the ecosystem that triggers the startin id: APOLLO_SV:00000131 name: reactive control strategy threshold def: "A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "reactiveControlMeasureThreshold" xsd:string property_value: IAO:0000600 "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc." xsd:string @@ -1127,7 +1132,7 @@ property_value: IAO:0000600 "Number of time steps it takes medical personnel to id: APOLLO_SV:00000135 name: ascertainment fraction comment: fraction of organisms (usually infected) that a surveillance system detects out of the total population -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "fractionInState" xsd:string property_value: IAO:0000600 "Fraction of all symptomatic individuals who will be ascertained" xsd:string @@ -1437,8 +1442,8 @@ name: antiviral treatment def: "A treatment with an antiviral drug." [] is_a: APOLLO_SV:00000318 ! drug treatment intersection_of: APOLLO_SV:00000318 ! drug treatment -intersection_of: OBI:0000293 CHEBI:36044 ! has_specified_input antiviral drug -relationship: OBI:0000293 CHEBI:36044 ! has_specified_input antiviral drug +intersection_of: OBI:0000293 CHEBI:36044 ! has specified input antiviral drug +relationship: OBI:0000293 CHEBI:36044 ! has specified input antiviral drug property_value: APOLLO_SV:0000040 "AntiviralTreatment" xsd:string property_value: IAO:0000600 "A treatment of a particular host with a particular antiviral drug with activity against a particular viral pathogen." xsd:string @@ -1540,7 +1545,7 @@ id: APOLLO_SV:00000184 name: infectious disease scenario def: "A dataset that represents at least one pathogen population (of a particular biological taxon) in one host population (of a particular biological taxon) in an ecosystem in a particular location at a particular point in time." [] comment: An infectious disease scenario contains counts of infections of a particular pathogen in a particular host in a particular ecosystem at a particular point in time, minimally. Agent-based ecosystems represent each host individually. \n\nThe infectious disease scenario typically also includes a lot of additional data about the ecosystem, including data about things like transmission probabililites, control measures, the immunity or other resistance status of host individuals, and so on. -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 APOLLO_SV:00000097 ! is about ecosystem property_value: APOLLO_SV:0000040 "InfectiousDiseaseScenario" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -1618,7 +1623,7 @@ is_obsolete: true id: APOLLO_SV:00000193 name: vaccination efficacy inferred def: "A data item inferring a vaccination efficacy based on epidemiological data." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "VaccinationEfficacyInferred" xsd:string property_value: IAO:0000600 "A data item inferring a vaccination efficacy based on epidemiological data." xsd:string @@ -1819,7 +1824,7 @@ property_value: IAO:0000600 "A probability distribution over a discrete random v id: APOLLO_SV:00000217 name: infection state data item def: "A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "infectionState" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen." xsd:string @@ -2031,7 +2036,7 @@ property_value: IAO:0000600 "A information content entity that specifies the dat id: APOLLO_SV:00000241 name: age range category def: "An information content entity specifying the upper and lower limit of a range of ages of continuants." [] -is_a: OBI:0001931 ! scalar value specification +is_a: OBI:0001931 property_value: APOLLO_SV:0000040 "AgeRangeCategoryDefinition" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "An information content entity specifying the upper and lower limit of a range of ages of continuants." xsd:string @@ -2700,8 +2705,8 @@ name: drug treatment def: "A treatment with a drug product." [] is_a: OGMS:0000090 ! treatment intersection_of: OGMS:0000090 ! treatment -intersection_of: OBI:0000293 DRON:00000005 ! has_specified_input clinical drug product -relationship: OBI:0000293 DRON:00000005 ! has_specified_input clinical drug product +intersection_of: OBI:0000293 DRON:00000005 ! has specified input clinical drug product +relationship: OBI:0000293 DRON:00000005 ! has specified input clinical drug product property_value: APOLLO_SV:0000040 "DrugTreatment" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Treatment with a drug." xsd:string @@ -3427,7 +3432,7 @@ property_value: IAO:0000600 "A population survey that assesses the presence (plu id: APOLLO_SV:00000397 name: infection case list def: "A data set that is a collection of case records." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: APOLLO_SV:0000040 "CaseList" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3437,7 +3442,7 @@ property_value: IAO:0000600 "A data set that is a collection of case records." x id: APOLLO_SV:00000398 name: infection case record def: "A data set whose data items are about a host and its participation in an infection and potentially other activities occuring in the same time interval as the infection." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: APOLLO_SV:0000040 "CaseRecord" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3474,13 +3479,14 @@ property_value: IAO:0000600 "An individual behavior of a mosquito (organism of f [Term] id: APOLLO_SV:00000402 -name: individual human behavior +name: obsolete individual human behavior def: "An individual behavior of a human being." [] -is_a: GO:0007610 ! behavior -property_value: APOLLO_SV:0000040 "HumanBehavior" xsd:string +is_a: oboInOwl:ObsoleteClass ! Obsolete Class property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An individual behavior of a human being." xsd:string +is_obsolete: true +replaced_by: BCIO:036000 [Term] id: APOLLO_SV:00000403 @@ -3687,7 +3693,7 @@ property_value: IAO:0000600 "A process of change in fecundity of females in a mo id: APOLLO_SV:00000422 name: confidence interval def: "A data item that specifies both an interval estimate centered around some sample statistic, and the probability that the process/method of obtaining the interval estimate's range of values will generate an interval that contains some unobserved population parameter of interest." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3763,7 +3769,7 @@ property_value: IAO:0000600 "A name of a temporal region that is systematized ac id: APOLLO_SV:00000430 name: ring diameter in meters def: "A scalar value specification that gives the diameter in meters of the circular area around which all organisms in a population are living will receive a vaccination as part of a ring vaccination control measure." [] -is_a: OBI:0001931 ! scalar value specification +is_a: OBI:0001931 property_value: APOLLO_SV:0000040 "ringDiameterInMeters" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3783,7 +3789,7 @@ property_value: IAO:0000600 "An epidemic simulator actions specification that sp id: APOLLO_SV:00000432 name: minimum value def: "A data item that specifies the smallest numerical value in a data set of scalar measurement data items." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "minimumValue" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3793,7 +3799,7 @@ property_value: IAO:0000600 "A data item that specifies the smallest numerical v id: APOLLO_SV:00000433 name: maximum value def: "A data item that specifies the largest numerical value in a data set of scalar measurement data itmes." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "maximumValue" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3922,7 +3928,7 @@ property_value: IAO:0000600 "A rate measurement datum that specifies the percent id: APOLLO_SV:00000446 name: ratio of outdoor to indoor ovisites def: "A data item that specifies, as a ratio, the total count of oviposition sites located externally to all places in a geographic region relative to the total count of oviposition sites located internally to some place in that geographic region." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "ratioOfOutdoorToIndoorOvisites" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3942,7 +3948,7 @@ property_value: IAO:0000600 "An information content entity that delimits an inte id: APOLLO_SV:00000448 name: standard deviation def: "A data item that specifies the dispersion of values around some parameter in a set of data, and whose values are standardized to express the same unit of measure as the parameter of interest." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "standardDeviation" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4164,7 +4170,7 @@ id: APOLLO_SV:00000470 name: probability def: "A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents." [] comment: The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'. -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "Probability" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4658,7 +4664,7 @@ id: APOLLO_SV:00000522 name: source code repository def: "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc." [] comment: Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection is_a: IAO:0000310 ! document relationship: has_part IAO:0000096 ! source code module property_value: IAO:0000111 "software source code version control repository" xsd:string @@ -4702,7 +4708,7 @@ id: APOLLO_SV:00000528 name: synthetic ecosystem data set def: "A data set that represents 1) one or more collections of organisms at some time and some geographical region; and optionally 2) the school facilities, workplace facilities, and health care facilities in that region." [] comment: The interactions between each organism as they move between these facilities may also be included in the data set. -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 APOLLO_SV:00000097 ! is about ecosystem property_value: APOLLO_SV:0000040 "SyntheticEcosystem" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -4732,7 +4738,7 @@ property_value: IAO:0000600 "A conditional probability whose value is dependent id: APOLLO_SV:00000531 name: epidemic threshold def: "A data item that specifies the number of susceptible organisms necessary for an epidemic to occur within a population." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4741,6 +4747,7 @@ id: APOLLO_SV:00000532 name: human travel def: "A geographical migration of an organism belonging to the species Homo sapiens." [] is_a: APOLLO_SV:00000480 ! geographical movement of organism +is_a: BCIO:036000 ! individual human behaviour property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4756,7 +4763,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000534 name: human mobility data item def: "A data item that is about one or more instances of human travel, and that specifies the geographical start location, geographical end location, and the geographical regions visited throughout the process." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4833,7 +4840,7 @@ property_value: IAO:0000600 "An objective specification whose endpoint is human id: APOLLO_SV:00000542 name: mortality data def: "A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 PCO:0000001 ! is about population property_value: IAO:0000111 "population mortality data set" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -4863,7 +4870,7 @@ property_value: IAO:0000600 "A planned process that is the realization of a dise id: APOLLO_SV:00000546 name: self-initiated travel avoidance behavior def: "Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition." [] -is_a: APOLLO_SV:00000402 ! individual human behavior +is_a: BCIO:036000 ! individual human behaviour property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition." xsd:string @@ -4872,7 +4879,7 @@ property_value: IAO:0000600 "Individual human behavior that involves either 1) r id: APOLLO_SV:00000547 name: social interaction data item def: "A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s)." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s)." xsd:string @@ -4935,7 +4942,7 @@ property_value: IAO:0000600 "A Susceptible-Infected-Resistant model that represe id: APOLLO_SV:00000554 name: disease surveillance data def: "A data set that is about some disease surveillance." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: OBI:0000312 APOLLO_SV:00000545 ! is specified output of disease surveillance property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4975,6 +4982,7 @@ property_value: IAO:0000118 "infectious disease forecasting software application id: APOLLO_SV:00000558 name: case series def: "An investigation that realizes the concretization of some disease state design and that has as an occurrent part some population survey that\nhas specified input some case definition." [] +is_a: OBI:0000011 ! planned process is_a: OBI:0000066 ! investigation property_value: APOLLO_SV:0000040 "CaseSeries" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -4985,7 +4993,7 @@ property_value: IAO:0000600 "An investigation following a disease state study de id: APOLLO_SV:00000559 name: case series data set def: "A data set that is the output of a case series investigation." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: OBI:0000312 APOLLO_SV:00000558 ! is specified output of case series property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4995,7 +5003,7 @@ property_value: IAO:0000600 "A data set that is the output of a case series inve id: APOLLO_SV:00000560 name: epidemic data set def: "A data set about an instance of an epidemic." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 APOLLO_SV:00000298 ! is about epidemic property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5047,7 +5055,7 @@ id: APOLLO_SV:00000566 name: data parsing def: "A data transformation that has a dataset, encoded in a particular data format specification, as input and extracts certain elements or parts of the dataset, typically into the volatile memory of a computer." [] is_a: OBI:0200000 ! data transformation -relationship: OBI:0000293 IAO:0000100 ! has_specified_input data set +relationship: OBI:0000293 IAO:0000100 ! has specified input homogenous data collection property_value: IAO:0000111 "data parsing process" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "data reading process" xsd:string @@ -5067,7 +5075,7 @@ property_value: IAO:0000118 "software for creating a synthetic ecosystem dataset id: APOLLO_SV:00000568 name: total fatal disease cases def: "A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "totalFatalCaseCount" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5089,7 +5097,7 @@ id: APOLLO_SV:00000570 name: employment status data item def: "A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions." [] comment: If an individual is a member of the labor force, the criteria that this status is selected from includes whether they are in the armed forces, employed and working, employed but absent from work for a week, and unemployed. The criteria for those not in the labor force includes whether the individual is a houseworker, suffering from a physical impairment that prevents them from working, in school, or other miscellaneous reasons. -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "employmentStatus" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5136,7 +5144,7 @@ property_value: IAO:0000118 "influenza-like illness" xsd:string id: APOLLO_SV:00000575 name: epidemic start week def: "A scalar value specification whose measurement unit label is 'week' and that is part of the first predicted data item that is greater than the epidemic threshold set for that data item." [] -is_a: OBI:0001931 ! scalar value specification +is_a: OBI:0001931 property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5145,7 +5153,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000576 name: epidemic peak week def: "A scalar value specification whose measurement unit label is 'week', and that is part of the epidemic peak intensity." [] -is_a: OBI:0001931 ! scalar value specification +is_a: OBI:0001931 property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5262,8 +5270,8 @@ name: website with data comment: This class was created for use case for MIDAS Digital Repository to index websites that have useful data in them, albeit rarely as machine-interpretable, downloadable datasets. Much of the data are locked in PDF or other text-based formats. is_a: FBcv:0000667 ! website intersection_of: FBcv:0000667 ! website -intersection_of: BFO:0000111 IAO:0000027 ! has proper continuant part at all times data item -relationship: BFO:0000111 IAO:0000027 ! has proper continuant part at all times data item +intersection_of: BFO:0000111 IAO:0000027 ! has proper continuant part at all times data entity +relationship: BFO:0000111 IAO:0000027 ! has proper continuant part at all times data entity property_value: IAO:0000111 "website that has data as a part" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5271,7 +5279,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000591 name: climate data set def: "A data set that is an aggregate of data items that are about an environmental system process (e.g., hydrological precipitation) or a participant in an environmental system process." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: IAO:0000111 "climate data set" xsd:string property_value: IAO:0000117 "Matt Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5289,7 +5297,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000593 name: abiotic ecosystem data set def: "A data set that is about some abiotic ecosystem or abiotic ecosystem element." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: IAO:0000111 "abiotic ecosystem data set" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "abiotic ecosystem dataset" xsd:string @@ -5354,8 +5362,8 @@ id: APOLLO_SV:00000599 name: infection acquisition dataset def: "A dataset that is about infectious disease acquisitions at particular times and particular places." [] comment: The dataset may include sites (e.g. types of facilities, rooms), events (e.g., church service whether in or outdoors), dates, times, geographical regions, etc. in which the sites/events are located, and so on. -is_a: IAO:0000100 ! data set -intersection_of: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection +intersection_of: IAO:0000100 ! homogenous data collection intersection_of: IAO:0000136 APOLLO_SV:00000115 ! is about infection acquisition relationship: IAO:0000136 APOLLO_SV:00000115 ! is about infection acquisition property_value: dc:creator http://orcid.org/0000-0002-9881-1017 @@ -5369,7 +5377,7 @@ id: APOLLO_SV:00000600 name: hospital stay dataset def: "A dataset that is about two or more hospital stays involving two or more patients." [] comment: The dataset may be limited to stays in one hospital, but hospital discharge datasets as compiled by state departments of health typically contain stays from multiple hospitals (typically every hospital) in the geographical region over which they have jurisdiction -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: dc:creator http://orcid.org/0000-0002-9881-1017 property_value: dc:date "2021-03-16T16:20:48Z" xsd:dateTime property_value: IAO:0000111 "dataset about hospital stays" xsd:string @@ -5382,7 +5390,7 @@ property_value: IAO:0000118 "hospitalization dataset" xsd:string id: APOLLO_SV:00000601 name: human daily movement def: "An individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time." [] -is_a: APOLLO_SV:00000402 ! individual human behavior +is_a: BCIO:036000 ! individual human behaviour property_value: dc:creator http://orcid.org/0000-0002-9881-1017 property_value: dc:date "2021-03-16T16:29:53Z" xsd:dateTime property_value: IAO:0000111 "human daily movement behavior" xsd:string @@ -5392,8 +5400,8 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000602 name: human daily movement data set def: "A data set that is about the human daily movement behavior of the individual huamns in a given population." [] -is_a: IAO:0000100 ! data set -intersection_of: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection +intersection_of: IAO:0000100 ! homogenous data collection intersection_of: IAO:0000136 APOLLO_SV:00000601 ! is about human daily movement relationship: IAO:0000136 APOLLO_SV:00000601 ! is about human daily movement property_value: dc:creator http://orcid.org/0000-0002-9881-1017 @@ -5406,8 +5414,8 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000603 name: potentially infectious contact data set def: "A data set that is about one or more potentially infectious contact processes in a population of host organisms." [] -is_a: IAO:0000100 ! data set -intersection_of: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection +intersection_of: IAO:0000100 ! homogenous data collection intersection_of: IAO:0000136 APOLLO_SV:00000405 ! is about potentially infectious contacting relationship: IAO:0000136 APOLLO_SV:00000405 ! is about potentially infectious contacting property_value: dc:creator http://orcid.org/0000-0002-9881-1017 @@ -5536,7 +5544,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000614 name: weather data set def: "A data set about the Earth's atmospheric weather" [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: dc:date "2022-09-18T18:34:00" xsd:string property_value: IAO:0000111 "data set about Earth's atmospheric weather" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5859,6 +5867,62 @@ is_a: APOLLO_SV:00000650 ! intent to have a ward vaccinated property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Intent to have one's child vaccinated." xsd:string +[Term] +id: APOLLO_SV:00000653 +name: human-to-human communicability +def: "A communicability among human beings (homo sapiens)." [] +is_a: IDO:0000623 ! communicability +property_value: APOLLO_SV:0000040 "HumanToHumanCommunicability" xsd:string +property_value: IAO:0000111 "communicability among human beings" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "The ability of a pathogen to transmit from one human host to another human host." xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 + +[Term] +id: APOLLO_SV:00000654 +name: historical scenario +def: "An infectious disease scenario that represents or reconstructs an outbreak or epidemic that actually occurred, usually constrained by observed data." [] +is_a: APOLLO_SV:00000184 ! infectious disease scenario +property_value: dc:contributor "John Levander" xsd:string +property_value: IAO:0000111 "historical infectious disease scenario date" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 +property_value: terms:created "2026-04-04T19:36:00Z" xsd:dateTime + +[Term] +id: APOLLO_SV:00000655 +name: hypothetical scenario +def: "An infectious disease scenario that represents a possible, assumed, projected, or counterfactual outbreak or epidemic, and does not need to correspond to a specific observed event." [] +is_a: APOLLO_SV:00000184 ! infectious disease scenario +property_value: dc:contributor "John Levander" xsd:string +property_value: IAO:0000111 "hypothetical infecctious disease scenario" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 +property_value: terms:created "2026-04-04T19:52:04Z" xsd:dateTime + +[Term] +id: APOLLO_SV:00000656 +name: antibody administration control strategy +def: "An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process." [] +is_a: APOLLO_SV:00000194 ! individual treatment control strategy +property_value: dc:contributor "Lucie Contamin" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: term_tracker_item https://github.com/ApolloDev/apollo-sv/issues/273 +property_value: terms:created "2026-07-13T14:13:40Z" xsd:dateTime +property_value: terms:creator https://orcid.org/0000-0002-9881-1017 + +[Term] +id: APOLLO_SV:00000657 +name: antibody administration census +def: "A population treatment census that is about one or more antibody administrations to organisms in a population." [] +is_a: APOLLO_SV:00000187 ! population treatment census +relationship: IAO:0000136 DRON:00000031 ! is about drug administration +property_value: dc:contributor "Lucie Contamin" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: term_tracker_item https://github.com/ApolloDev/apollo-sv/issues/273 +property_value: terms:created "2026-07-13T13:52:47Z" xsd:dateTime +property_value: terms:creator https://orcid.org/0000-0002-9881-1017 + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification @@ -5885,10 +5949,9 @@ id: APOLLO_SV:00000796 name: dataset creating def: "A planned process that has a data set as its specified output." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -intersection_of: OBI:0000011 ! planned process -intersection_of: OBI:0000299 IAO:0000100 ! has specified output data set -relationship: OBI:0000299 IAO:0000100 ! has specified output data set +intersection_of: COB:0000035 ! completely executed planned process +intersection_of: OBI:0000299 IAO:0000100 ! has specified output homogenous data collection +relationship: OBI:0000299 IAO:0000100 ! has specified output homogenous data collection property_value: IAO:0000111 "creating a data set" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "data set creation" xsd:string @@ -5967,6 +6030,35 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "The sensitivity of the process or system that detects organisms that have undergone a particular treatment" xsd:string is_obsolete: true +[Term] +id: BCIO:006158 +name: habitual behaviour +def: "An that results from a learnt stimulus-behaviour co-occurrence." [] +comment: A learnt stimulus-behaviour co-occurrence can lead to activation or execution of a habitual behaviour.\n\nHabitual behaviour can be an MoA or outcome depending on how 'habitual behaviour' is described in an intervention. The Behaviour Change-Intervention Ontology includes the class 'outcome behaviour' (definition: Human behavior that is an intervention outcome.), which would not be an MoA. When an intervention targets a habitual behaviour to achieve an outcome behaviour, the former qualifies as an MoA. +is_a: BCIO:036000 ! individual human behaviour +property_value: IAO:0000112 " \"Habit\" in the Theory of Interpersonal Behavior" xsd:string +property_value: IAO:0000112 "\"Habits\" in the Motivation-Opportunities-Abilities" xsd:string +property_value: IAO:0000114 "Published" xsd:string + +[Term] +id: BCIO:026022 +name: educational facility +def: "A facility in which formal education is provided to a student population." [] +is_a: OMRSE:00000062 ! facility +property_value: IAO:0000114 "Published" xsd:string + +[Term] +id: BCIO:036000 +name: individual human behaviour +def: "A of a human that involves co-ordinated contraction of striated muscles controlled by the brain." [] +comment: it is concerned with moving skeletal parts to which it is usually attached.' (https://www.collinsdictionary.com/dictionary/english/striped-muscle) +is_a: OGMS:0000060 ! bodily process +property_value: APOLLO_SV:0000040 "HumanBehavior" xsd:string +property_value: IAO:0000112 "Also referred to in definitions as human behaviour or just behaviour." xsd:string +property_value: IAO:0000112 "walks for 15 mins/day, never eats meat, attends school daily" xsd:string +property_value: IAO:0000114 "Published" xsd:string +property_value: IAO:0000118 "human behaviour" xsd:string + [Term] id: BFO:0000001 name: entity @@ -6303,9 +6395,7 @@ property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:stri property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011", IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} @@ -6597,8 +6687,18 @@ property_value: IAO:0000116 "Includes virus - we will later have a class for cel [Term] id: COB:0000035 name: completely executed planned process -is_a: BFO:0000015 ! process +is_a: COB:0000082 ! planned process disjoint_from: GO:0008150 ! biological_process +property_value: IAO:0000111 "completely executed planned process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/cob.owl + +[Term] +id: COB:0000082 +name: planned process +def: "A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/cob.owl [Term] id: DOID:0060478 @@ -6703,6 +6803,15 @@ def: "A drug product that is bearer of a clinical drug role." [] comment: We changed the label to 'clinical drug product' because it was clear that the part of the definition re: bearer of a "clinical drug role" made it such. Other drugs don't have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf "drug product", which also required changing the definition here. is_a: DRON:00000074 ! drug product property_value: IAO:0000117 "William Hogan" xsd:string +property_value: terms:creator "https://orcid.org/0000-0002-9881-1017" xsd:anyURI + +[Term] +id: DRON:00000031 +name: drug administration +def: "A treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism." [] +is_a: OGMS:0000090 ! treatment +property_value: IAO:0000111 "administration of a drug product to an organism" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] id: DRON:00000074 @@ -6713,12 +6822,13 @@ is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-6378-1703 property_value: terms:contributor https://orcid.org/0000-0002-5039-2052 +property_value: terms:creator "http://orcid.org/0000-0002-9881-1017" xsd:string [Term] id: EFO:0004600 name: genomic data def: "Genomic data is data about the genomes of an organism." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 OBI:0100026 ! is about organism property_value: IAO:0000117 "James Malone" xsd:string @@ -6888,41 +6998,11 @@ subset: camcur is_a: IAO:0000310 ! document property_value: IAO:0000412 "http://purl.org/obo/owl/flybase_vocab" xsd:string -[Term] -id: GEO:000000001 -name: geopolitical entity -def: "An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii)" [] -comment: In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions. -is_a: oboInOwl:ObsoleteClass ! Obsolete Class -property_value: IAO:0000117 "William R. Hogan" xsd:string -is_obsolete: true - -[Term] -id: GEO:000000002 -name: obsolete group of governmental organizations -def: "An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on." [] -comment: taken over by GEO_0000000401 -is_a: BFO:0000004 ! independent continuant -property_value: IAO:0000111 "obsolete aggregate of governmental organizations" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -is_obsolete: true - -[Term] -id: GEO:000000003 -name: nation -def: "A geopolitical entity that is self contained and recognizes no higher political authority than itself." [] -is_a: oboInOwl:ObsoleteClass ! Obsolete Class -property_value: IAO:0000117 "William R. Hogan" xsd:string -is_obsolete: true - [Term] id: GEO:000000004 name: subnational entity def: "a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority" [] is_a: GEO:000000400 ! governmental organization -intersection_of: GEO:000000400 ! governmental organization -intersection_of: GEO:000000329 GEO:000000396 ! is subordinate authority of sovereign state -relationship: GEO:000000329 GEO:000000396 ! is subordinate authority of sovereign state property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -6945,60 +7025,6 @@ is_a: GEO:000000004 ! subnational entity property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string -[Term] -id: GEO:000000007 -name: aggregate of major administrative subdivisions -def: "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common." [] -comment: Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. -is_a: GEO:000000337 ! aggregate of governmental organizations -relationship: BFO:0000075 GEO:000000005 ! is aggregate of major administrative subdivision -property_value: IAO:0000117 "Amanda Hicks" xsd:string - -[Term] -id: GEO:000000008 -name: aggregate of dependencies -def: "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." [] -comment: Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. -is_a: GEO:000000337 ! aggregate of governmental organizations -relationship: BFO:0000075 GEO:000000006 ! is aggregate of geopolitical dependency -property_value: IAO:0000117 "Amanda Hicks" xsd:string - -[Term] -id: GEO:000000334 -name: subcontinental land mass -is_a: GEO:000000375 ! land mass -relationship: BFO:0000137 GEO:000000374 ! proper part of continuant at all times continent - -[Term] -id: GEO:000000335 -name: contiguous land mass -comment: per the definition of 'contiguous' of "being in actual contact : touching along a boundary or at a point", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island.\n\nAt some point, we need an 'adjacent to' relation if BFO doesn't provide it.\n\nOne question is whether this class encompasses fiat parts of islands. -is_a: GEO:000000334 ! subcontinental land mass -property_value: IAO:0000118 "contiguous continental land mass" xsd:string - -[Term] -id: GEO:000000337 -name: aggregate of governmental organizations -def: "An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members.\n" [] -is_a: BFO:0000004 ! independent continuant -relationship: BFO:0000075 GEO:000000400 ! is aggregate of governmental organization -property_value: IAO:0000117 "William R. Hogan" xsd:string - -[Term] -id: GEO:000000357 -name: contiguous island land mass -def: "A subcontinental land mass that is part of an island and includes part of the land surface of the island." [] -comment: It cannot be a part of the island, for example, that is below water. -is_a: GEO:000000334 ! subcontinental land mass -property_value: IAO:0000117 "William R. Hogan" xsd:string - -[Term] -id: GEO:000000369 -name: aggregate of contiguous land masses -is_a: GEO:000000375 ! land mass -is_a: GEO:000000377 ! aggregate of geographical entities -relationship: BFO:0000075 GEO:000000375 ! is aggregate of land mass - [Term] id: GEO:000000370 name: geographical entity @@ -7030,45 +7056,6 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers." xsd:string -[Term] -id: GEO:000000373 -name: body of water -is_a: GEO:000000372 ! geographical region - -[Term] -id: GEO:000000374 -name: continent -is_a: GEO:000000375 ! land mass - -[Term] -id: GEO:000000375 -name: land mass -is_a: GEO:000000372 ! geographical region - -[Term] -id: GEO:000000376 -name: island -is_a: GEO:000000334 ! subcontinental land mass - -[Term] -id: GEO:000000377 -name: aggregate of geographical entities -def: "An object aggregate of geographical entities" [] -is_a: BFO:0000027 ! object_aggregate -relationship: BFO:0000075 GEO:000000370 ! is aggregate of geographical entity - -[Term] -id: GEO:000000378 -name: aggregate of geographical features -is_a: GEO:000000377 ! aggregate of geographical entities -relationship: BFO:0000075 GEO:000000371 ! is aggregate of geographical feature - -[Term] -id: GEO:000000390 -name: aggregate of islands -is_a: GEO:000000369 ! aggregate of contiguous land masses -relationship: BFO:0000075 GEO:000000376 ! is aggregate of island - [Term] id: GEO:000000391 name: geopoli organization @@ -7117,13 +7104,6 @@ property_value: IAO:0000118 "nation" xsd:string property_value: IAO:0000118 "nation state" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Sovereign_state" xsd:string -[Term] -id: GEO:000000399 -name: supranational entity -comment: e.g., the EU -is_a: GEO:000000400 ! governmental organization -property_value: IAO:0000117 "Amanda Hicks" xsd:string - [Term] id: GEO:000000400 name: governmental organization @@ -7132,56 +7112,6 @@ comment: IMPORTANT: The label "geopolitical organization" was previously used fo is_a: OBI:0000245 ! organization property_value: IAO:0000117 "Amanda Hicks" xsd:string -[Term] -id: GEO:000000401 -name: aggregate of geopolitical organizations -def: "An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common" [] -is_a: BFO:0000004 ! independent continuant -relationship: BFO:0000075 GEO:000000391 ! is aggregate of geopoli organization -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000117 "William R. Hogan\n" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: GEO:000000402 -name: obsolete aggregate of dependencies -def: "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." [] -comment: Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. -is_a: GEO:000000337 ! aggregate of governmental organizations -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string -is_obsolete: true - -[Term] -id: GEO:000000403 -name: obsolete aggregate of major administrative subdivisions -def: "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common" [] -comment: Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. -is_a: GEO:000000337 ! aggregate of governmental organizations -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string -is_obsolete: true - -[Term] -id: GEO:000000404 -name: aggregate of sovereign states -def: "An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common" [] -comment: examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc. -is_a: GEO:000000337 ! aggregate of governmental organizations -relationship: BFO:0000075 GEO:000000396 ! is aggregate of sovereign state -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: GEO:000000787 -name: geodetic coordinate measurement datum -def: "A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum." [] -comment: latitude and longitude are key subtypes -is_a: IAO:0000109 ! measurement datum -property_value: IAO:0000111 "geodetic coordinate measurement datum" xsd:string -property_value: IAO:0000117 "Josh Hanna" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string - [Term] id: GEO:000000788 name: geodetic datum @@ -7193,12 +7123,6 @@ property_value: IAO:0000117 "Josh Hanna" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000119 "Wikipedia: https://en.wikipedia.org/wiki/Geodetic_datum\n\nDate accessed: 2015-04-13" xsd:string -[Term] -id: GEO:000000789 -name: plane angle measurement unit label -is_a: IAO:0000003 ! measurement unit label -property_value: IAO:0000111 "planar angular measurement unit label" xsd:string - [Term] id: GEO:000000797 name: de jure sovereign state @@ -7270,6 +7194,7 @@ synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -7335,6 +7260,7 @@ is_a: GO:0048609 ! multicellular organismal reproductive process intersection_of: GO:0007610 ! behavior intersection_of: GO:0048609 ! multicellular organismal reproductive process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23491" xsd:anyURI created_by: jl creation_date: 2012-09-19T16:01:37Z @@ -7348,6 +7274,7 @@ subset: gocheck_do_not_annotate xref: Wikipedia:Sexual_reproduction is_a: APOLLO_SV:00000651 ! reproduction is_a: GO:0022414 ! reproductive process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22929" xsd:anyURI [Term] id: GO:0019954 @@ -7358,6 +7285,7 @@ synonym: "parthenogenesis" RELATED [Wikipedia:Parthenogenesis] xref: Wikipedia:Asexual_reproduction is_a: APOLLO_SV:00000651 ! reproduction is_a: GO:0022414 ! reproductive process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22929" xsd:anyURI [Term] id: GO:0022414 @@ -7378,6 +7306,7 @@ subset: goslim_plant_ribbon synonym: "single organism reproductive process" RELATED [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI created_by: jl creation_date: 2012-09-19T15:56:06Z @@ -7394,6 +7323,7 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -7417,7 +7347,10 @@ synonym: "symbiotic interaction between host and organism" RELATED [] synonym: "symbiotic interaction between organisms" RELATED [] synonym: "symbiotic interaction between species" RELATED [] synonym: "symbiotic process" RELATED [] +xref: Reactome:R-HSA-9839923 "Dengue Virus Infection" is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14807" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] id: GO:0044409 @@ -7458,6 +7391,7 @@ xref: Reactome:R-HSA-173107 "Binding and entry of HIV virion" is_a: GO:0051701 ! biological process involved in interaction with host is_a: GO:0051704 ! multi-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18563" xsd:anyURI [Term] id: GO:0044419 @@ -7473,6 +7407,7 @@ synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] xref: Reactome:R-HSA-9824443 "Parasitic Infection Pathways" is_a: GO:0008150 ! biological_process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] id: GO:0048609 @@ -7485,6 +7420,7 @@ synonym: "organismal reproductive process" BROAD [] synonym: "reproductive process in a multicellular organism" EXACT [] xref: Reactome:R-HSA-1474165 "Reproduction" is_a: GO:0022414 ! reproductive process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI [Term] id: GO:0051234 @@ -7512,8 +7448,10 @@ synonym: "growth of symbiont in host organelle" NARROW [] synonym: "growth of symbiont in host vacuole" NARROW [] synonym: "interaction with host" EXACT [] xref: Reactome:R-HSA-9635486 "Infection with Mycobacterium tuberculosis" +xref: Reactome:R-HSA-9640148 "Infection with Enterobacteria" xref: Reactome:R-HSA-9658195 "Leishmania infection" is_a: GO:0044403 ! biological process involved in symbiotic interaction +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] id: GO:0051704 @@ -7536,17 +7474,15 @@ property_value: IAO:0000119 "OBI_0000349" xsd:string [Term] id: IAO:0000003 name: measurement unit label -def: "A data item label that denotes a unit of measure." [] -is_a: IAO:0000009 ! data item label +def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." [] +is_a: IAO:0000009 ! datum label property_value: IAO:0000111 "measurement unit label" xsd:string property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string -property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." xsd:string property_value: IAO:0000116 "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: IAO:0000005 @@ -7600,18 +7536,14 @@ is_obsolete: true [Term] id: IAO:0000009 -name: data item label +name: datum label def: "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" [] is_a: IAO:0000030 ! information content entity -property_value: IAO:0000111 "data item label" xsd:string property_value: IAO:0000111 "datum label" xsd:string -property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n" xsd:string property_value: IAO:0000117 "GROUP: IAO" xsd:string -property_value: IAO:0000118 "datum label" xsd:string property_value: IAO:0000232 "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. \n" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: IAO:0000010 @@ -7730,9 +7662,10 @@ property_value: IAO:0000119 "OBI_0000058" xsd:string [Term] id: IAO:0000027 -name: data item -def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] +name: data entity +def: "An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity +property_value: IAO:0000111 "data entity" xsd:string property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -7745,6 +7678,7 @@ property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000118 "data" xsd:string +property_value: IAO:0000118 "data item" xsd:string [Term] id: IAO:0000028 @@ -7799,14 +7733,12 @@ id: IAO:0000032 name: scalar measurement datum def: "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." [] is_a: IAO:0000109 ! measurement datum -property_value: IAO:0000111 "scalar measurement datum" xsd:string property_value: IAO:0000112 "10 feet. 3 ml." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" xsd:string property_value: IAO:0000116 "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: IAO:0000033 @@ -8077,21 +8009,22 @@ property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000119 "OBI_0000187" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/172 [Term] id: IAO:0000100 -name: data set +name: homogenous data collection def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." [] -is_a: IAO:0000027 ! data item -property_value: IAO:0000111 "data set" xsd:string +is_a: IAO:0001000 ! data collection +property_value: IAO:0000111 "homogenous data collection" xsd:string property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string property_value: IAO:0000116 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000118 "data set" xsd:string property_value: IAO:0000119 "group:OBI" xsd:string -property_value: IAO:0000119 "OBI_0000042" xsd:string [Term] id: IAO:0000101 @@ -8110,7 +8043,7 @@ property_value: IAO:0000119 "OBI_0000030" xsd:string id: IAO:0000102 name: data about an ontology part def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000111 "data about an ontology part" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string @@ -8153,7 +8086,7 @@ is_obsolete: true id: IAO:0000109 name: measurement datum def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000111 "measurement datum" xsd:string property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -8161,7 +8094,6 @@ property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:st property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 "group:OBI" xsd:string property_value: IAO:0000119 "OBI_0000305" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: IAO:0000128 @@ -8206,7 +8138,7 @@ property_value: IAO:0000118 "batch number" xsd:string id: IAO:0000140 name: setting datum def: "A settings datum is a datum that denotes some configuration of an instrument." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2/3/2009 Feedback from OBI\n\nThis should be a \"setting specification\". There is a question of whether it is information about a realizable or not.\n\nPro other specification are about realizables.\nCons sometimes specifies a quality which is not a realizable." xsd:string property_value: IAO:0000116 "Alan grouped these in placeholder for the moment. Name by analogy to measurement datum." xsd:string @@ -8483,7 +8415,7 @@ property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "published document" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/232 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/232 [Term] id: IAO:0000312 @@ -8529,7 +8461,7 @@ property_value: IAO:0000112 "The profusion of high-throughput instruments and th property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "precis" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000316 @@ -8544,7 +8476,7 @@ property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "background" xsd:string property_value: IAO:0000118 "introduction" xsd:string property_value: IAO:0000118 "overview" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000317 @@ -8563,7 +8495,7 @@ property_value: IAO:0000118 "experimental section" xsd:string property_value: IAO:0000118 "method" xsd:string property_value: IAO:0000118 "methodology" xsd:string property_value: IAO:0000118 "methods" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000318 @@ -8588,7 +8520,7 @@ property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "discussion" xsd:string property_value: IAO:0000118 "discussion section" xsd:string property_value: IAO:0000118 "discussions" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000320 @@ -8604,7 +8536,7 @@ property_value: IAO:0000118 "literature cited" xsd:string property_value: IAO:0000118 "reference" xsd:string property_value: IAO:0000118 "reference list" xsd:string property_value: IAO:0000118 "references" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000321 @@ -8643,7 +8575,7 @@ property_value: IAO:0000118 "authors' contributions" xsd:string property_value: IAO:0000118 "authors' roles" xsd:string property_value: IAO:0000118 "contributions by the authors" xsd:string property_value: IAO:0000118 "contributorship" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000324 @@ -8658,7 +8590,7 @@ property_value: IAO:0000118 "acknowledgement" xsd:string property_value: IAO:0000118 "acknowledgements" xsd:string property_value: IAO:0000118 "acknowledgment" xsd:string property_value: IAO:0000118 "acknowledgments" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000325 @@ -8672,7 +8604,7 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "endnote" xsd:string property_value: IAO:0000118 "footnotes" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000326 @@ -8697,7 +8629,7 @@ property_value: IAO:0000118 "supplementary information" xsd:string property_value: IAO:0000118 "supplementary material" xsd:string property_value: IAO:0000118 "supplementary materials" xsd:string property_value: IAO:0000118 "supporting information" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000327 @@ -8740,7 +8672,7 @@ property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string id: IAO:0000400 name: cartesian spatial coordinate datum def: "A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude" [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity relationship: IAO:0000219 BFO:0000018 ! denotes zero-dimensional spatial region property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617" xsd:string @@ -8861,9 +8793,8 @@ id: IAO:0000443 name: data item extraction from journal article def: "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000013 ! has_specified_input journal article -relationship: OBI:0000299 IAO:0000027 ! has specified output data item +relationship: OBI:0000293 IAO:0000013 ! has specified input journal article +relationship: OBI:0000299 IAO:0000027 ! has specified output data entity property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string @@ -8871,12 +8802,12 @@ property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string id: IAO:0000444 name: publishing process def: "A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free." [] -is_a: OBI:0000011 ! planned process +is_a: COB:0000035 ! completely executed planned process property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Jie Zheng" xsd:string property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Publishing" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/232 property_value: IAO:0000234 "VEuPathDB" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/232 [Term] id: IAO:0000445 @@ -8886,16 +8817,15 @@ is_a: IAO:0000310 ! document property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "EFO_0001795 in preparation" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/232 property_value: IAO:0000234 "VEuPathDB" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/232 [Term] id: IAO:0000572 name: documenting def: "A planned process in which a document is created or added to by including the specified input in it." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity +relationship: OBI:0000293 IAO:0000030 ! has specified input information content entity relationship: OBI:0000299 IAO:0000310 ! has specified output document property_value: IAO:0000112 "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -8921,7 +8851,6 @@ id: IAO:0000574 name: assigning a centrally registered identifier def: "A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity" [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process relationship: OBI:0000299 IAO:0000577 ! has specified output centrally registered identifier symbol relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry property_value: IAO:0000112 "A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned." xsd:string @@ -8936,8 +8865,8 @@ property_value: IAO:0000118 "assigning a CRID" xsd:string id: IAO:0000575 name: associating information with a centrally registered identifier in its registry def: "A planned process in which a CRID registry associates an information content entity with a CRID symbol" [] -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol +is_a: COB:0000035 ! completely executed planned process +relationship: OBI:0000293 IAO:0000577 ! has specified input centrally registered identifier symbol relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry property_value: IAO:0000112 "Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. " xsd:string property_value: IAO:0000114 IAO:0000120 @@ -9000,15 +8929,14 @@ property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "CRID registry" xsd:string property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0000580 name: looking up a centrally registered identifier def: "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol" [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol +relationship: OBI:0000293 IAO:0000577 ! has specified input centrally registered identifier symbol relationship: OBI:0000299 IAO:0000030 ! has specified output information content entity relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry property_value: IAO:0000112 "Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. " xsd:string @@ -9031,7 +8959,7 @@ property_value: IAO:0000114 IAO:0000123 id: IAO:0000584 name: time sampled measurement data set def: "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: has_part IAO:0000582 ! time stamped measurement datum property_value: IAO:0000112 "pmid:20604925 - time-lapse live cell microscopy" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -9110,7 +9038,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "abbreviation textual entity" xsd:string property_value: IAO:0000112 "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nBAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000606 @@ -9133,8 +9061,8 @@ property_value: IAO:0000118 "list of abbreviations used" xsd:string property_value: IAO:0000118 "non-standard abbreviations" xsd:string property_value: IAO:0000118 "nonstandard abbreviations" xsd:string property_value: IAO:0000118 "nonstandard abbreviations and acronyms" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000607 @@ -9149,8 +9077,8 @@ property_value: IAO:0000118 "author information" xsd:string property_value: IAO:0000118 "authors’ information" xsd:string property_value: IAO:0000118 "biographies" xsd:string property_value: IAO:0000118 "contributor information" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000608 @@ -9160,7 +9088,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "author information textual entity" xsd:string property_value: IAO:0000112 "From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/):\n\nIT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000609 @@ -9175,7 +9103,7 @@ property_value: IAO:0000118 "author summary" xsd:string property_value: IAO:0000118 "summary" xsd:string property_value: IAO:0000118 "synopsis" xsd:string property_value: IAO:0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000610 @@ -9186,7 +9114,7 @@ property_value: IAO:0000111 "author summary textual entity" xsd:string property_value: IAO:0000112 "From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/):\n\n\nThe search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000611 @@ -9203,8 +9131,8 @@ property_value: IAO:0000118 "data archiving" xsd:string property_value: IAO:0000118 "data availability" xsd:string property_value: IAO:0000118 "data availability statement" xsd:string property_value: IAO:0000118 "data sharing statement" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000612 @@ -9214,7 +9142,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "availability textual entity" xsd:string property_value: IAO:0000112 "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\nProject home page:http://krux.googlecode.com" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000613 @@ -9227,7 +9155,7 @@ property_value: IAO:0000112 "The section labelled 'case report' in a typical sci property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "case presentation" xsd:string property_value: IAO:0000118 "case report" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000614 @@ -9237,7 +9165,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "case report textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/):\n\nThe patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000615 @@ -9253,7 +9181,7 @@ property_value: IAO:0000118 "conclusion" xsd:string property_value: IAO:0000118 "conclusions" xsd:string property_value: IAO:0000118 "findings" xsd:string property_value: IAO:0000118 "summary" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000616 @@ -9279,8 +9207,8 @@ property_value: IAO:0000118 "disclosure of conflict of interest" xsd:string property_value: IAO:0000118 "disclosure of potential conflicts of interest" xsd:string property_value: IAO:0000118 "duality of interest" xsd:string property_value: IAO:0000118 "statement of interest" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000617 @@ -9290,7 +9218,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "conflict of interest statement" xsd:string property_value: IAO:0000112 "SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] " xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000618 @@ -9302,7 +9230,7 @@ property_value: IAO:0000111 "consent section" xsd:string property_value: IAO:0000112 "The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "consent" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000619 @@ -9312,7 +9240,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "consent textual entity" xsd:string property_value: IAO:0000112 "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nWritten informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000620 @@ -9327,8 +9255,8 @@ property_value: IAO:0000118 "ethical approval" xsd:string property_value: IAO:0000118 "ethical requirements" xsd:string property_value: IAO:0000118 "ethics" xsd:string property_value: IAO:0000118 "ethics statement" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000621 @@ -9339,7 +9267,7 @@ relationship: IAO:0000136 OBI:0500000 ! is about study design property_value: IAO:0000111 "ethical approval textual entity" xsd:string property_value: IAO:0000112 "From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):\n\nThe NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000622 @@ -9351,7 +9279,7 @@ property_value: IAO:0000111 "figures section" xsd:string property_value: IAO:0000112 "The section labelled 'figures' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "figures" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000623 @@ -9373,8 +9301,8 @@ property_value: IAO:0000118 "role of the funding source" xsd:string property_value: IAO:0000118 "source of funding" xsd:string property_value: IAO:0000118 "sources of funding" xsd:string property_value: IAO:0000118 "study funding" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000624 @@ -9384,7 +9312,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "funding souce declaration textual entity" xsd:string property_value: IAO:0000112 "From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/):\n\nThis study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000625 @@ -9408,8 +9336,8 @@ property_value: IAO:0000118 "future research directions" xsd:string property_value: IAO:0000118 "future studies" xsd:string property_value: IAO:0000118 "future work" xsd:string property_value: IAO:0000118 "outlook" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000626 @@ -9419,7 +9347,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "future directions textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/):\n\nIn the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000627 @@ -9431,7 +9359,7 @@ property_value: IAO:0000111 "genome announcement section" xsd:string property_value: IAO:0000112 "The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "genome announcement" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000628 @@ -9441,7 +9369,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "genome announcement textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/):\n\nHere we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000629 @@ -9451,7 +9379,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "keyword textual entity" xsd:string property_value: IAO:0000112 "From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/):\n\nExon orthology; alternative splicing; exon duplication; intron-exon structure." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000630 @@ -9463,7 +9391,7 @@ property_value: IAO:0000111 "keywords section" xsd:string property_value: IAO:0000112 "The section labelled 'keywords' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "keywords" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000631 @@ -9478,7 +9406,7 @@ property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "limitations" xsd:string property_value: IAO:0000118 "study limitations" xsd:string property_value: IAO:0000119 "Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000632 @@ -9489,7 +9417,7 @@ property_value: IAO:0000111 "study limitations textual entity" xsd:string property_value: IAO:0000112 "Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). \n\nOwing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000119 "Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000633 @@ -9500,7 +9428,7 @@ property_value: IAO:0000111 "materials section" xsd:string property_value: IAO:0000112 "The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "materials" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000634 @@ -9511,7 +9439,7 @@ property_value: IAO:0000111 "notes section" xsd:string property_value: IAO:0000112 "The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "notes" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000635 @@ -9522,7 +9450,7 @@ relationship: has_part IAO:0000636 ! patients textual entity property_value: IAO:0000111 "patients section" xsd:string property_value: IAO:0000112 "The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000636 @@ -9532,7 +9460,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "patients textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/):\n\nBetween January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000637 @@ -9545,7 +9473,7 @@ property_value: IAO:0000112 "The section labelled 'pre-publication history' in a property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "notice of republication" xsd:string property_value: IAO:0000118 "pre-publication history" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000638 @@ -9555,7 +9483,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "pre-publication history textual entity" xsd:string property_value: IAO:0000112 "From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/):\n\nThe pre-publication history for this paper can be accessed here:\nhttp://www.biomedcentral.com/1471-2253/13/33/prepub" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000639 @@ -9568,7 +9496,7 @@ property_value: IAO:0000112 "The section labelled 'related work' in a typical sc property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "related literature" xsd:string property_value: IAO:0000118 "related work" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000640 @@ -9578,7 +9506,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "related work textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/):\n\nOur work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).\n\n" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000641 @@ -9590,7 +9518,7 @@ property_value: IAO:0000111 "requirements section" xsd:string property_value: IAO:0000112 "The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/)." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "requirements" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000642 @@ -9600,7 +9528,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "requirements textual entity" xsd:string property_value: IAO:0000112 "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\n• Operating systems: Platform independent\n\n• Programming language: Matlab, R, Python\n\n• Other requirements: None\n\n• License: GNU GPL v3\n\n• Any restrictions to use by non-academics: None" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000643 @@ -9610,7 +9538,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "statistical analysis textual entity" xsd:string property_value: IAO:0000112 "From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/):\n\nData were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000644 @@ -9622,7 +9550,7 @@ property_value: IAO:0000111 "statistical analysis section" xsd:string property_value: IAO:0000112 "The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "statistical analysis" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000645 @@ -9634,7 +9562,7 @@ property_value: IAO:0000111 "tables section" xsd:string property_value: IAO:0000112 "The section labelled 'tables' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "tables" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000646 @@ -9663,8 +9591,7 @@ id: IAO:0000650 name: database extract, transform, and load process def: "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity +relationship: OBI:0000293 IAO:0000030 ! has specified input information content entity relationship: OBI:0000299 IAO:0000030 ! has specified output information content entity property_value: foaf:page https://en.wikipedia.org/wiki/Extract,_transform,_load property_value: IAO:0000111 "database extract, transform, and load process" xsd:string @@ -9673,8 +9600,17 @@ property_value: IAO:0000116 "Alan Ruttenberg 12/21/16: We don't define database property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string property_value: IAO:0000118 "ETL" xsd:string property_value: IAO:0000119 "WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/187 property_value: isDefinedBy https://github.com/information-artifact-ontology/IAO +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/187 + +[Term] +id: IAO:0000651 +name: title section +def: "the section of the document where the title appears" [] +is_a: IAO:0000314 ! document part +property_value: IAO:0000116 "This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself." xsd:string +property_value: IAO:0000117 "Charles Tapley Hoyt" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/286" xsd:anyURI [Term] id: IAO:0000701 @@ -9686,8 +9622,8 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/prisma/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000702 @@ -9701,8 +9637,8 @@ property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/consort/" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/prisma/" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/strobe/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000703 @@ -9716,8 +9652,8 @@ property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/consort/" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/prisma/" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/strobe-nut/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000704 @@ -9729,8 +9665,8 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/strobe/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000705 @@ -9742,8 +9678,8 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.ncbi.nlm.nih.gov/books/NBK262175/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000706 @@ -9755,8 +9691,8 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "DOI: 10.1097/PRS.0b013e3181de24bc" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000707 @@ -9769,8 +9705,8 @@ property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000117 "PERSON: Tim Beck" xsd:string property_value: IAO:0000118 "visual abstract" xsd:string property_value: IAO:0000119 "https://www.elsevier.com/authors/journal-authors/graphical-abstract" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 property_value: IAO:0000234 "Biomedical literature NLP project" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000708 @@ -9786,7 +9722,18 @@ property_value: IAO:0000118 "Open Researcher and Contributor Identifier" xsd:str property_value: IAO:0000118 "ORCiD" xsd:string property_value: IAO:0000118 "ORCID ID" xsd:string property_value: IAO:0000119 "https://orcid.org/" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/259" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/259" xsd:string + +[Term] +id: IAO:0001000 +name: data collection +def: "A data entity that consists of multiple data entities." [] +is_a: IAO:0000027 ! data entity +property_value: IAO:0000111 "data collection" xsd:string +property_value: IAO:0000117 "Sebastian Duesing" xsd:string +property_value: IAO:0000118 "data set" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/283" xsd:string +property_value: term_tracker_item "https://github.com/obi-ontology/obi/issues/1877" xsd:string [Term] id: IAO:0020000 @@ -9804,7 +9751,7 @@ property_value: IAO:0000111 "identifier" xsd:string property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "proper name" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020001 @@ -9816,15 +9763,14 @@ property_value: dc:creator "Mathias Brochhausen" xsd:string property_value: IAO:0000112 "alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems" xsd:string property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Grapheme" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020010 name: identifier creating process def: "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -intersection_of: OBI:0000011 ! planned process +intersection_of: COB:0000035 ! completely executed planned process intersection_of: OBI:0000299 IAO:0020000 ! has specified output identifier relationship: OBI:0000299 IAO:0020000 ! has specified output identifier property_value: dc:creator "Mathias Brochhausen" xsd:string @@ -9832,7 +9778,7 @@ property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "dubbing process" xsd:string property_value: IAO:0000118 "naming" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020015 @@ -9843,7 +9789,7 @@ is_a: IAO:0020000 ! identifier property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Personal_name" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020016 @@ -9854,7 +9800,7 @@ property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "first name" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Given_name" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020017 @@ -9866,7 +9812,7 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "last name" xsd:string property_value: IAO:0000118 "surname" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Family_name" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020020 @@ -9888,7 +9834,7 @@ property_value: IAO:0000118 "code system" xsd:string property_value: IAO:0000118 "codeset" xsd:string property_value: IAO:0000118 "coding system" xsd:string property_value: IAO:0000118 "controlled vocabulary" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0021003 @@ -15250,7 +15196,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/dideo/dev/dideo.owl" [Term] id: OBI:0000011 name: planned process -def: "A process that realizes a plan which is the concretization of a plan specification." [] +def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string @@ -15275,7 +15221,7 @@ property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string id: OBI:0000066 name: investigation def: "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)." [] -is_a: OBI:0000011 ! planned process +is_a: COB:0000035 ! completely executed planned process property_value: IAO:0000111 "investigation" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl @@ -15336,7 +15282,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: OBI:0000471 name: study design execution def: "a planned process that carries out a study design" [] -is_a: OBI:0000011 ! planned process +is_a: COB:0000035 ! completely executed planned process property_value: IAO:0000111 "study design execution" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl @@ -15374,7 +15320,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: OBI:0000674 name: center value def: "A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "median" xsd:string property_value: IAO:0000111 "center value" xsd:string property_value: IAO:0000114 IAO:0000125 @@ -15387,8 +15333,8 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: OBI:0000679 name: average value def: "A data item that is produced as the output of an averaging data transformation and represents the average value of the input data." [] -is_a: IAO:0000027 ! data item -intersection_of: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity +intersection_of: IAO:0000027 ! data entity intersection_of: OBI:0000312 OBI:0200170 ! is specified output of averaging data transformation relationship: OBI:0000312 OBI:0200170 ! is specified output of averaging data transformation property_value: APOLLO_SV:0000040 "mean" xsd:string @@ -15527,34 +15473,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: OBI:0001847 "study description" xsd:string property_value: OBI:0001886 "project description" xsd:string -[Term] -id: OBI:0001620 -name: latitude coordinate measurement datum -def: "A measurement datum that is the measure of the latitude coordinate of a site." [] -is_a: GEO:000000787 ! geodetic coordinate measurement datum -property_value: dc:source "NIAID GSCID-BRC" xsd:string -property_value: IAO:0000111 "latitude coordinate measurement datum" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string -property_value: IAO:0000118 "latitude" xsd:string -property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: OBI:0001886 "Specimen Collection Location - Latitude" xsd:string - -[Term] -id: OBI:0001621 -name: longitude coordinate measurement datum -def: "A measurement datum that is the measure of the longitude coordinate of a site." [] -is_a: GEO:000000787 ! geodetic coordinate measurement datum -property_value: dc:source "NIAID GSCID-BRC" xsd:string -property_value: IAO:0000111 "longitude coordinate measurement datum" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string -property_value: IAO:0000118 "longitude" xsd:string -property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: OBI:0001886 "Specimen Collection Location - Longitude" xsd:string - [Term] id: OBI:0001628 name: investigation identifier @@ -15582,28 +15500,6 @@ property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: OBI:0001886 "grant ID" xsd:string -[Term] -id: OBI:0001931 -name: scalar value specification -def: "A value specification that consists of two parts: a numeral and a unit label" [] -is_a: OBI:0001933 ! value specification -property_value: IAO:0000111 "scalar value specification" xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0001933 -name: value specification -def: "An information content entity that specifies a value within a classification scheme or on a quantitative scale." [] -is_a: IAO:0000030 ! information content entity -property_value: IAO:0000111 "value specification" xsd:string -property_value: IAO:0000112 "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass." xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000116 "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement." xsd:string -property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - [Term] id: OBI:0001958 name: systematic review study design @@ -15857,7 +15753,9 @@ def: "A process in which at least one bodily component of an organsim participat comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060 is_a: BFO:0000015 ! process relationship: BFO:0000167 OGMS:0000087 ! has participant at all times extended organism +property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://www.jbiomedsem.com/content/1/1/10" xsd:string +property_value: IAO:0000232 "creation date: 2009-06-23T11:53:49Z" xsd:string [Term] id: OGMS:0000063 @@ -16167,10 +16065,11 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] id: OMRSE:00000064 name: school facility -def: "A facility that is run by a school organization and is the bearer of a school function." [] -is_a: OMRSE:00000062 ! facility +def: "An educational facility that is run by a school organization and is the bearer of a school function." [] +is_a: BCIO:026022 ! educational facility relationship: RO:0000053 OMRSE:00000053 ! bearer of school function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 [Term] id: OMRSE:00000065 @@ -16257,13 +16156,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string [Term] id: PATO:0000117 -name: size -namespace: quality -def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [] -subset: attribute_slim -subset: scalar_slim is_a: PATO:0000051 ! morphology -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string [Term] id: PATO:0000122 @@ -16357,18 +16250,6 @@ property_value: IAO:0000111 "physical object quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string -[Term] -id: PATO:0001323 -name: area -namespace: quality -def: "A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent." [] -comment: MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area. -subset: attribute_slim -subset: mpath_slim -subset: scalar_slim -is_a: PATO:0001709 ! 2-D extent -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - [Term] id: PATO:0001708 name: 1-D extent @@ -16376,17 +16257,7 @@ namespace: quality def: "A size quality inhering in an bearer by virtue of the bearer's extension in one dimension." [] subset: attribute_slim synonym: "1-D size" EXACT [] -is_a: PATO:0000117 ! size -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0001709 -name: 2-D extent -namespace: quality -def: "A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions." [] -subset: attribute_slim -synonym: "2-D size" EXACT [] -is_a: PATO:0000117 ! size +is_a: PATO:0000117 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string [Term] @@ -16429,7 +16300,7 @@ name: population def: "A collection of organisms, all of the same species, that live in the same place." [] comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used. is_a: PCO:0000018 ! collection of organisms of the same species -relationship: BFO:0000177 APOLLO_SV:00000104 ! part of continuant at all times biotic ecosystem +relationship: BFO:0000177 APOLLO_SV:00000104 ! biotic ecosystem property_value: APOLLO_SV:0000040 "Population" xsd:string property_value: IAO:0000116 "Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific." xsd:string property_value: IAO:0000119 "ISBN:0878932739" xsd:string @@ -16529,7 +16400,7 @@ property_value: STATO:0000032 "" xsd:string id: STATO:0000258 name: variable def: "A variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "variable" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string @@ -16617,8 +16488,6 @@ id: UBERON:0000071 name: death stage def: "End of the life of an organism." [XAO:0000437] subset: common_anatomy -subset: human_subset -subset: mouse_subset synonym: "death" RELATED [] xref: XAO:0000437 xref: XtroDO:0000085 @@ -16630,8 +16499,6 @@ name: life cycle stage def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [https://orcid.org/0000-0002-6601-2165] subset: common_anatomy subset: efo_slim -subset: human_subset -subset: mouse_subset subset: upper_level synonym: "developmental stage" NARROW [] synonym: "stage" NARROW [] @@ -16840,8 +16707,6 @@ id: UBERON:0035943 name: life cycle temporal boundary def: "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity." [https://orcid.org/0000-0002-6601-2165] subset: common_anatomy -subset: human_subset -subset: mouse_subset subset: upper_level is_a: BFO:0000035 ! process boundary @@ -16855,6 +16720,7 @@ property_value: IAO:0000412 "http://purl.org/obo/owl/unit" xsd:string [Term] id: UO:0000001 name: length unit +def: "A unit which is a standard measure of the distance between two points." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "length unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl @@ -16862,6 +16728,7 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000002 name: mass unit +def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "mass unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl @@ -16869,22 +16736,13 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000003 name: time unit +def: "A unit which is a standard measure of the dimension in which events occur in sequence." [] is_a: IAO:0000003 ! measurement unit label property_value: APOLLO_SV:0000040 "unitOfTime" xsd:string property_value: IAO:0000111 "time unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: IAO:0000412 http://purl.org/obo/owl/UO -[Term] -id: UO:0000047 -name: area unit -namespace: unit.ontology -def: "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [] -subset: unit_group_slim -is_a: IAO:0000003 ! measurement unit label -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uo.owl" xsd:string -created_by: george gkoutos - [Term] id: UO:0000186 name: dimensionless unit @@ -16980,7 +16838,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/vo.owl" xsd:string [Term] id: oboInOwl:ObsoleteClass name: Obsolete Class -property_value: IAO:0000412 "http://www.geneontology.org/formats/oboInOwl" xsd:string [Term] id: oboInOwl:Subset @@ -17138,27 +16995,6 @@ property_value: IAO:0000111 "is aggregate of" xsd:string property_value: IAO:0000118 "aggregate of" xsd:string property_value: IAO:0000118 "aggregate_of" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string -inverse_of: GEO:000000328 ! is in aggregate - -[Typedef] -id: BFO:0000083 -name: occupies spatial region at some time -property_value: BFO:0000179 "located-at-r_st" xsd:string -property_value: BFO:0000180 "occupiesSpatialRegionAt" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)" xsd:string -property_value: IAO:0000116 "BFO2 Reference: independent continuant" xsd:string -property_value: IAO:0000116 "BFO2 Reference: spatial region" xsd:string -property_value: IAO:0000600 "b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])" xsd:string -property_value: IAO:0000601 "every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])" xsd:string -property_value: IAO:0000601 "if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])" xsd:string -property_value: IAO:0000602 "(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] " xsd:string -property_value: IAO:0000602 "(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] " xsd:string -property_value: IAO:0000602 "(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000004 ! independent continuant -range: BFO:0000006 ! spatial region -inverse_of: BFO:0000123 ! has spatial occupant at some time [Typedef] id: BFO:0000108 @@ -17167,25 +17003,11 @@ name: exists at [Typedef] id: BFO:0000110 name: has continuant part at all times -def: "[copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)" [] -property_value: BFO:0000179 "c-has-part_at" xsd:string -property_value: BFO:0000180 "hasContinuantPartAt" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000602 "(iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl is_transitive: true [Typedef] id: BFO:0000111 name: has proper continuant part at all times -def: "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001" [] -property_value: BFO:0000179 "c-has-ppart_at" xsd:string -property_value: BFO:0000180 "hasProperContinuantPartAt" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl is_transitive: true is_a: BFO:0000110 ! has continuant part at all times @@ -17243,18 +17065,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl is_a: BFO:0000117 ! has occurrent part -[Typedef] -id: BFO:0000123 -name: has spatial occupant at some time -property_value: BFO:0000179 "r-location-of_st" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region" xsd:string -property_value: IAO:0000600 "[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000006 ! spatial region -range: BFO:0000004 ! independent continuant - [Typedef] id: BFO:0000132 name: part of occurrent @@ -17291,20 +17101,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl is_a: BFO:0000138 ! proper part of occurrent is_a: BFO:0000139 ! temporal part of -[Typedef] -id: BFO:0000137 -name: proper part of continuant at all times -def: "b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001])" [] -property_value: BFO:0000179 "c-ppart-of_at" xsd:string -property_value: BFO:0000180 "properContinuantPartOfAt" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000602 "(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -is_transitive: true -is_a: BFO:0000177 ! part of continuant at all times -inverse_of: BFO:0000187 ! has continuant part at all times that part exists - [Typedef] id: BFO:0000138 name: proper part of occurrent @@ -17406,39 +17202,6 @@ property_value: IAO:0000602 "(forall (x y z t) (if (and (specificallyDependsOnAt property_value: IAO:0000602 "(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] " xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Typedef] -id: BFO:0000177 -name: part of continuant at all times -def: "[copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)" [] -property_value: BFO:0000179 "c-part-of_at" xsd:string -property_value: BFO:0000180 "continuantPartOfAt" xsd:string -property_value: IAO:0000112 "Mary’s arm continuant_part_of Mary in the time of her life prior to her operation" xsd:string -property_value: IAO:0000112 "the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])" xsd:string -property_value: IAO:0000116 "BFO2 Reference: continuant" xsd:string -property_value: IAO:0000116 "BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000600 "b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])" xsd:string -property_value: IAO:0000601 "continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])" xsd:string -property_value: IAO:0000601 "continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])" xsd:string -property_value: IAO:0000601 "continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])" xsd:string -property_value: IAO:0000601 "continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])" xsd:string -property_value: IAO:0000601 "continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])" xsd:string -property_value: IAO:0000601 "if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])" xsd:string -property_value: IAO:0000602 "(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] " xsd:string -property_value: IAO:0000602 "(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] " xsd:string -property_value: IAO:0000602 "(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -is_reflexive: true -is_transitive: true - [Typedef] id: BFO:0000181 name: has proper temporal part @@ -17462,48 +17225,19 @@ domain: BFO:0000040 ! material entity range: BFO:0000015 ! process [Typedef] -id: BFO:0000187 -name: has continuant part at all times that part exists -def: "forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)" [] -property_value: BFO:0000179 "c-has-part-object_at" xsd:string -property_value: IAO:0000112 "[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation" xsd:string -property_value: IAO:0000112 "[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region." xsd:string -property_value: IAO:0000116 "This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000600 "[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: GEO:000000328 -name: is in aggregate - -[Typedef] -id: GEO:000000329 -name: is subordinate authority of -def: "A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2." [] -comment: \n'is subordinate authority of'\nDomain: governing organization\nRange: governing organization\nFormal properties: transitive, anti-symmetric, irreflexive\nNatural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2. -domain: GEO:000000400 ! governmental organization -range: GEO:000000400 ! governmental organization - -[Typedef] -id: GEO:000000336 -name: has jurisdiction in -comment: It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c.\n\nin other words, it is perfectly fine to say:\na disjoint b\nc has_jurisdiction_in a\nc has_jurisdiction_in b\n\notherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it "United States territory", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities. -domain: GEO:000000400 ! governmental organization -range: GEO:000000375 ! land mass -is_asymmetric: true +id: IAO:0000011 +name: is directed towards +def: "A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality." [] +comment: In the definition source, the relation is called 'is_about'. To avoid confusion with the existing "is about" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion. +property_value: IAO:0000112 "One of my mental representations is directed towards the Pacific Ocean." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person: William Hogan" xsd:string +property_value: IAO:0000119 "https://ceur-ws.org/Vol-1515/regular10.pdf" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/285 [Typedef] id: IAO:0000039 name: has measurement unit label -def: "A relation between a value specification and its unit of measurement." [] -property_value: IAO:0000111 "has measurement unit label" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string range: IAO:0000003 ! measurement unit label is_functional: true is_a: has_part ! has part @@ -17531,7 +17265,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/iao.owl" xsd:string domain: IAO:0000030 ! information content entity [Typedef] @@ -17552,7 +17285,7 @@ name: mentioned by def: "Inverse of the relation 'mentions'" [] property_value: dc:date "2022-01-28T07:20:08Z" xsd:dateTime property_value: IAO:0000117 http://orcid.org/0000-0002-8844-9165 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/250 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/250 [Typedef] id: IAO:0000219 @@ -17609,7 +17342,7 @@ id: IAO:0000235 name: denoted by def: "inverse of the relation 'denotes'" [] property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/206 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/206 domain: BFO:0000001 ! entity range: IAO:0000030 ! information content entity @@ -17685,10 +17418,9 @@ name: results_in [Typedef] id: OBI:0000293 -name: has_specified_input -def: "The inverse property of is_specified_input_of" [] -property_value: IAO:0000111 "has_specified_input" xsd:string -property_value: IAO:0000111 "has_specified_input" xsd:string +name: has specified input +def: "The inverse property of is specified input of" [] +property_value: IAO:0000111 "has specified input" xsd:string property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string @@ -17697,37 +17429,26 @@ property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -domain: OBI:0000011 ! planned process +domain: COB:0000035 ! completely executed planned process is_a: RO:0000057 ! has participant +inverse_of: OBI:0000295 ! is specified input of [Typedef] id: OBI:0000295 -name: is_specified_input_of -property_value: IAO:0000111 "is_specified_input_of" xsd:string -property_value: IAO:0000112 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -is_a: RO:0000056 ! participates in +name: is specified input of [Typedef] id: OBI:0000299 name: has specified output def: "The inverse property of is specified output of" [] property_value: IAO:0000111 "has specified output" xsd:string -property_value: IAO:0000111 "has_specified_output" xsd:string -property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: COB:0000035 ! completely executed planned process -domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000312 ! is specified output of @@ -17741,15 +17462,11 @@ id: OBI:0000312 name: is specified output of def: "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] property_value: IAO:0000111 "is specified output of" xsd:string -property_value: IAO:0000111 "is_specified_output_of" xsd:string -property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string range: COB:0000035 ! completely executed planned process -range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] @@ -17763,16 +17480,6 @@ property_value: IAO:0000119 "PPPB branch derived" xsd:string property_value: IAO:0000232 "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -[Typedef] -id: OBI:0001938 -name: has value specification -def: "A relation between an information content entity and a value specification that specifies its value." [] -property_value: IAO:0000111 "has value specification" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string -property_value: IAO:0000119 "OBI" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - [Typedef] id: OBIB:0000732 name: owns @@ -17866,7 +17573,6 @@ property_value: IAO:0000112 "this blood clot participates in this blood coagulat property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string property_value: IAO:0000118 "participates_in" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: RO:0000057 ! has participant @@ -17883,7 +17589,6 @@ property_value: IAO:0000112 "this investigation has participant this investigato property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant @@ -18448,6 +18153,7 @@ def: "p is causally upstream of, positive effect q iff p is casually upstream of comment: 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: terms:creator https://orcid.org/0000-0002-6601-2165 is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -18457,6 +18163,7 @@ name: causally upstream of, negative effect def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: terms:creator https://orcid.org/0000-0002-6601-2165 is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect diff --git a/apollo_sv-full.owl b/apollo_sv-full.owl index 6478dce..0e48097 100644 --- a/apollo_sv-full.owl +++ b/apollo_sv-full.owl @@ -27,7 +27,7 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -43,7 +43,7 @@ C87985BA-6A8A-483A-A6B6-63975101F672 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). - 2026-03-13 + 2026-07-19 @@ -189,120 +189,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - - - US State Two Digit Identifier - - - - - - - - US State Two Letter Abbreviation - - - - - - - - US State Ens Identifier - - - - - - - - UN Numerical Code - - - - - - - - ISO 3166-1-alpha-3 code - - - - - - - - ISO 3166-1-alpha-2 code - - - - - - - - Proposed Apollo Location Code - - - - - - - - ISO 3166-2 code - - - - - - - - geonameid - integer id of record in geonames database - geonameid - - - - - - - - geonames admin1 code - fipscode (subject to change to iso code), see exceptions below, see file admin1Codes.txt for display names of this code; varchar(20) - admin1 code - - - - - - - - geonames admin2 code - code for the second administrative division, a county in the US, see file admin2Codes.txt; varchar(80) - admin2 code - - - - - - - - geonames admin3 code - code for third level administrative division, varchar(20) - admin3 code - - - - - - - - geonames admin4 code - code for fourth level administrative division, varchar(20) - admin4 code - - - - @@ -315,7 +201,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. editor preferred label editor preferred term editor preferred term - editor preferred term~editor preferred label @@ -462,6 +347,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label alternative term @@ -513,14 +399,28 @@ We also have the outstanding issue of how to aim different definitions to differ + term tracker item term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588 + A URL for a request or discussion of an ontology term. + An IRI or similar locator for a request or discussion of an ontology term. An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + IAO:0000233 + external + term_tracker_item + term_tracker_item + The 'tracker item' can associate a tracker with a specific ontology term. The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item term tracker item + @@ -893,14 +793,224 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + + 2025-06-02 + preferred label for community + + + + + + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initialisms + + + 2023-03-03 + abbreviation + + + + + + + + + A synonym type for describing ambiguous synonyms + + + 2023-03-03 + ambiguous synonym + + + + + + + + + A synonym type for describing dubious synonyms + + + 2023-03-03 + dubious synonym + + + + + + + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + + 2023-03-03 + layperson synonym + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + + 2023-03-03 + UK spelling synonym + + + + + + + + + A synonym type for common misspellings + + + 2023-03-03 + misspelling + + + + + + + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + + 2023-03-03 + misnomer + + + + + + + + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + + 2023-07-25 + previous name + + + + + + + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + + 2023-07-27 + legal name + + + + + + + + + CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label + The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + + + 2023-09-30 + INN + International Nonproprietary Name + + + + + + + + + nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis + A synonym type for describing Latin term synonyms. + + + 2023-10-12 + latin term + + + + + + + + + NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. + A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + + + 2023-11-01 + acronym + + + + + + + + + The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`. + Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf. + + + 2025-09-17 + has ontology hierarchical property + + + + + + + + A serial number such as "12324X"; a stop sign; a written proper name such as "OBI + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + + + 2024-03-25 + has symbol + + + + @@ -1150,30 +1260,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - - - - - - - - - - - - - - - - - - - @@ -1255,14 +1341,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - - - @@ -1381,6 +1459,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + @@ -1466,7 +1556,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + 2024-03-18 database_cross_reference has cross-reference @@ -1475,9 +1567,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - has_definition - + @@ -1626,6 +1716,23 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + - - - - - - located-at-r_st - occupiesSpatialRegionAt - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) - BFO2 Reference: independent continuant - BFO2 Reference: spatial region - b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) - every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002]) - if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001]) - (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] - (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] - (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] - - occupies spatial region at some time - - - - @@ -2028,17 +2109,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - c-has-part_at - hasContinuantPartAt - [copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) - b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'. - [copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times' - http://purl.obolibrary.org/obo/bfo.owl - (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] - has continuant part at all times @@ -2049,12 +2120,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - c-has-ppart_at - hasProperContinuantPartAt - b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001 - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'. - http://purl.obolibrary.org/obo/bfo.owl - has proper continuant part at all times @@ -2134,22 +2199,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - r-location-of_st - [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) - [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant - [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region - [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) - - has spatial occupant at some time - - - - @@ -2197,19 +2246,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - c-ppart-of_at - properContinuantPartOfAt - b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001]) - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'. - http://purl.obolibrary.org/obo/bfo.owl - (iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] - - proper part of continuant at all times - + @@ -2371,39 +2408,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - c-part-of_at - continuantPartOfAt - Mary’s arm continuant_part_of Mary in the time of her life prior to her operation - the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. - [copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. - BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) - BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. - BFO2 Reference: continuant - BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. - [copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' - http://purl.obolibrary.org/obo/bfo.owl - b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) - continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) - continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) - continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) - continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) - continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) - if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) - (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] - (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] - (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] - (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] - (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] - (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] - (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] - - part of continuant at all times - + @@ -2441,72 +2446,17 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - c-has-part-object_at - [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation - [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. - forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) - This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' - [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. - [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) - [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. - [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant - [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. - http://purl.obolibrary.org/obo/bfo.owl - [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) - - has continuant part at all times that part exists - - - - - + - - is in aggregate - - - - - - - - - - - A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2. - -'is subordinate authority of' -Domain: governing organization -Range: governing organization -Formal properties: transitive, anti-symmetric, irreflexive -Natural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2. - is subordinate authority of - - - - - - - - - - - - It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c. - -in other words, it is perfectly fine to say: -a disjoint b -c has_jurisdiction_in a -c has_jurisdiction_in b - -otherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it "United States territory", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities. - a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories. - if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b. - has jurisdiction in + + One of my mental representations is directed towards the Pacific Ocean. + + A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality. + person: William Hogan + https://ceur-ws.org/Vol-1515/regular10.pdf + + In the definition source, the relation is called 'is_about'. To avoid confusion with the existing "is about" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion. + is directed towards @@ -2517,9 +2467,6 @@ otherwise, we'd end up creating some mereological sum of all the islands, c - has measurement unit label - A relation between a value specification and its unit of measurement. - http://purl.obolibrary.org/obo/obi.owl has measurement unit label @@ -2567,12 +2514,10 @@ Pattern of magnetic domains on scattered pieces of a hard disk platter as mark w - This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. - is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. @@ -2580,7 +2525,6 @@ We will try to build it back up by elaborating the various subproperties that ar Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy - http://purl.obolibrary.org/obo/iao.owl is about @@ -2873,26 +2817,20 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - has_specified_input - has_specified_input + + + has specified input see is_input_of example_of_usage - The inverse property of is_specified_input_of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - http://purl.obolibrary.org/obo/obi.owl - has_specified_input + has specified input @@ -2900,14 +2838,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - is_specified_input_of - some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - - Alan Ruttenberg - PERSON:Bjoern Peters - http://purl.obolibrary.org/obo/obi.owl - is_specified_input_of + is specified input of @@ -2915,29 +2846,18 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - has specified output - has_specified_output - has_specified_output The inverse property of is specified output of - The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot - http://purl.obolibrary.org/obo/obi.owl has specified output - has_specified_output @@ -2956,19 +2876,13 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is specified output of - is_specified_output_of - is_specified_output_of A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - http://purl.obolibrary.org/obo/obi.owl is specified output of - is_specified_output_of @@ -2991,16 +2905,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - has value specification - - A relation between an information content entity and a value specification that specifies its value. - PERSON: James A. Overton - OBI - http://purl.obolibrary.org/obo/obi.owl - has value specification - + @@ -3126,7 +3031,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - @@ -3136,7 +3040,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in - http://purl.obolibrary.org/obo/obi.owl participates in @@ -3145,7 +3048,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - @@ -3165,7 +3067,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://purl.obolibrary.org/obo/obi.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -4212,6 +4113,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. + 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 @@ -4226,6 +4128,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. + causally upstream of, negative effect @@ -5710,9 +5613,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A relation between a scalar measurement data item and a number that quantifies it. - The range should probably not be restricted to "float". It makes sense to set it to "real". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now. - http://purl.obolibrary.org/obo/obi.owl has measurement value @@ -5762,6 +5662,61 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + "Habit" in the Theory of Interpersonal Behavior + "Habits" in the Motivation-Opportunities-Abilities + Published + An <individual human behaviour> that results from a learnt stimulus-behaviour co-occurrence. + A learnt stimulus-behaviour co-occurrence can lead to activation or execution of a habitual behaviour. + +Habitual behaviour can be an MoA or outcome depending on how 'habitual behaviour' is described in an intervention. The Behaviour Change-Intervention Ontology includes the class 'outcome behaviour' (definition: Human behavior that is an intervention outcome.), which would not be an MoA. When an intervention targets a habitual behaviour to achieve an outcome behaviour, the former qualifies as an MoA. + habitual behaviour + + + + + + + + + Published + A facility in which formal education is provided to a student population. + educational facility + + + + + + + + + Also referred to in definitions as human behaviour or just behaviour. + walks for 15 mins/day, never eats meat, attends school daily + Published + A <bodily process> of a human that involves co-ordinated contraction of striated muscles controlled by the brain. + A bodily process of a human that involves co-ordinated contraction of striated muscles controlled by the brain. + human behaviour + HumanBehavior + it is concerned with moving skeletal parts to which it is usually attached.' (https://www.collinsdictionary.com/dictionary/english/striped-muscle) + The class human behaviour [BCIO:042000] has been made obsolete. If you want to refer to the behaviour of an individual, refer to individual human behaviour . If you want to refer to the behaviour of a group, refer to population behaviour. + +Striated muscles referred to in the definition do not ordinarily involve cardiac muscles. + +Behaviours are usually in response to an internal or external stimuli. + +Every behaviour is associated with mental processes, but not every mental process is associated with behaviour. For instance, a verbal communication behaviour will involve mental processes to produce speech. However, mental processes associated with listening can occur without a person performing a behaviour. + +'behaviours' can involve a series of activities (e.g., more granular behaviours). + +'A 'striated muscle' can defined as 'a type of contractile tissue that is marked by transverse striations + individual human behaviour + + + + @@ -5953,7 +5908,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire - + @@ -5969,7 +5924,6 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire - @@ -6575,7 +6529,7 @@ can't recall whether we should use process or processual_entity for future - + @@ -6584,7 +6538,6 @@ can't recall whether we should use process or processual_entity for future - @@ -7855,7 +7808,6 @@ The time step value and unit are specified using a scalar value specification. - @@ -15133,13 +15085,14 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + An individual behavior of a human being. Matthew Diller William R. Hogan An individual behavior of a human being. - HumanBehavior - individual human behavior + + obsolete individual human behavior + true @@ -17003,6 +16956,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s + A geographical migration of an organism belonging to the species Homo sapiens. Matthew Diller @@ -17183,7 +17137,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition. Matthew Diller William R. Hogan @@ -17378,6 +17332,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s + @@ -18202,7 +18157,7 @@ has specified input some case definition. - + human daily movement behavior An individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time. William R. Hogan @@ -19158,6 +19113,111 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + + + + + + + + + + + + + + + + + + + + + + + + communicability among human beings + A communicability among human beings (homo sapiens). + William R. Hogan + The ability of a pathogen to transmit from one human host to another human host. + HumanToHumanCommunicability + + human-to-human communicability + + + + + + + + + historical infectious disease scenario date + An infectious disease scenario that represents or reconstructs an outbreak or epidemic that actually occurred, usually constrained by observed data. + William R. Hogan + John Levander + + 2026-04-04T19:36:00Z + historical scenario + + + + + + + + + hypothetical infecctious disease scenario + An infectious disease scenario that represents a possible, assumed, projected, or counterfactual outbreak or epidemic, and does not need to correspond to a specific observed event. + William R. Hogan + John Levander + + 2026-04-04T19:52:04Z + hypothetical scenario + + + + + + + + + An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process. + William R. Hogan + + Lucie Contamin + 2026-07-13T14:13:40Z + + antibody administration control strategy + + + + + + + + + + + + + + + A population treatment census that is about one or more antibody administrations to organisms in a population. + William R. Hogan + + Lucie Contamin + 2026-07-13T13:52:47Z + + antibody administration census + + + + @@ -19197,7 +19257,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si - + @@ -19206,7 +19266,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si - @@ -20208,18 +20267,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects @@ -20864,13 +20911,27 @@ By "similar vaccines" we typically mean same pathogen, but could be si - + + completely executed planned process + completely executed planned process + + + + + planned process + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + + planned process + + + + @@ -20997,12 +21058,25 @@ By "similar vaccines" we typically mean same pathogen, but could be si A drug product that is bearer of a clinical drug role. William Hogan + https://orcid.org/0000-0002-9881-1017 We changed the label to 'clinical drug product' because it was clear that the part of the definition re: bearer of a "clinical drug role" made it such. Other drugs don't have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf "drug product", which also required changing the definition here. clinical drug product + + + + + administration of a drug product to an organism + A treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism. + William R. Hogan + drug administration + + + + @@ -21011,6 +21085,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si William R. Hogan + http://orcid.org/0000-0002-9881-1017 The "intention" part is important because of situations, such as that with phenylephrine, where it was not effective for the labeled use. Even when a drug is proven effective for a particular indication, it might not be therapeutic for every indivdiual to whom it is administered. The psychoactive effect is added for illicit drugs such as crack cocaine. We are including prophylactic and diagnostic effects / usage under the more general heading of 'therapeutic'. @@ -21245,92 +21320,10 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - - - - An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii) - William R. Hogan - In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions. - geopolitical entity - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - obsolete aggregate of governmental organizations - An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on. - William R. Hogan - taken over by GEO_0000000401 - obsolete group of governmental organizations - true - - - - - - - - - A geopolitical entity that is self contained and recognizes no higher political authority than itself. - William R. Hogan - nation - true - - - - - - - - - - - - - - - - - - - - - a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority Amanda Hicks William R. Hogan @@ -21366,180 +21359,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common. - Amanda Hicks - Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. - aggregate of major administrative subdivisions - group of major administrative subdivisions - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common. - Amanda Hicks - Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. - aggregate of dependencies - group of dependencies - - - - - - - - - - - - - - - subcontinental land mass - - - - - - - - - contiguous continental land mass - per the definition of 'contiguous' of "being in actual contact : touching along a boundary or at a point", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island. - -At some point, we need an 'adjacent to' relation if BFO doesn't provide it. - -One question is whether this class encompasses fiat parts of islands. - contiguous land mass - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members. - - William R. Hogan - aggregate of governmental organizations - - - - - - - - - A subcontinental land mass that is part of an island and includes part of the land surface of the island. - William R. Hogan - It cannot be a part of the island, for example, that is below water. - contiguous island land mass - - - - - - - - - - - - - - - - - - - - - - aggregate of contiguous land masses - - - - @@ -21591,106 +21410,6 @@ Thus, we are attempting to define things generally enough that they could be reu - - - - - body of water - - - - - - - - - continent - - - - - - - - - land mass - - - - - - - - - island - - - - - - - - - - - - - - - - - - - - - An object aggregate of geographical entities - aggregate of geographical entities - - - - - - - - - - - - - - - - - - - - - aggregate of geographical features - - - - - - - - - - - - - - - - - - - - - aggregate of islands - - - - @@ -21779,190 +21498,6 @@ Note: this definition was taken over from "geopolitical organization". - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common - Amanda Hicks - William R. Hogan - - http://purl.obolibrary.org/obo/omrse.owl - aggregate of geopolitical organizations - - - - - - - - - An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common. - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. - obsolete aggregate of dependencies - true - - - - - - - - - An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. - obsolete aggregate of major administrative subdivisions - true - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common - William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl - examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc. - aggregate of sovereign states - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - geodetic coordinate measurement datum - A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum. - Josh Hanna - William R. Hogan - latitude and longitude are key subtypes - geodetic coordinate measurement datum - - - - @@ -21980,16 +21515,6 @@ Date accessed: 2015-04-13 - - - - - planar angular measurement unit label - plane angle measurement unit label - - - - @@ -22079,6 +21604,7 @@ Date accessed: 2015-04-13 A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. + https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z @@ -22275,6 +21801,7 @@ Date accessed: 2015-04-13 The specific behavior of an organism that is associated with reproduction. + https://github.com/geneontology/go-ontology/issues/23491 jl 2012-09-19T16:01:37Z @@ -22306,6 +21833,7 @@ Date accessed: 2015-04-13 A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). + https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Sexual_reproduction biological_process GO:0019953 @@ -22328,6 +21856,7 @@ Date accessed: 2015-04-13 A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells. + https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Asexual_reproduction biological_process parthenogenesis @@ -22357,6 +21886,7 @@ Date accessed: 2015-04-13 A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. + https://github.com/geneontology/go-ontology/issues/27054 jl 2012-09-19T15:56:06Z GO:0019952 @@ -22391,6 +21921,7 @@ Date accessed: 2015-04-13 Any biological process, occurring at the level of a multicellular organism, pertinent to its function. + https://github.com/geneontology/go-ontology/issues/27189 jl 2012-09-19T16:07:47Z GO:0044707 @@ -22421,10 +21952,13 @@ Date accessed: 2015-04-13 A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts. + https://github.com/geneontology/go-ontology/issues/14807 + https://github.com/geneontology/go-ontology/issues/20191 GO:0043298 GO:0044404 GO:0072519 GO:0085031 + Reactome:R-HSA-9839923 commensalism host-pathogen interaction parasitism @@ -22447,6 +21981,12 @@ Date accessed: 2015-04-13 GOC:cc PMID:31257129 + + + + Reactome:R-HSA-9839923 + Dengue Virus Infection + @@ -22457,6 +21997,7 @@ Date accessed: 2015-04-13 Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction. Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. + https://github.com/geneontology/go-ontology/issues/18563 GO:0030260 GO:0044411 @@ -22550,6 +22091,7 @@ Date accessed: 2015-04-13 Any process evolved to enable an interaction with an organism of a different species. + https://github.com/geneontology/go-ontology/issues/20191 Reactome:R-HSA-9824443 interaction with another species interspecies interaction @@ -22582,6 +22124,7 @@ Date accessed: 2015-04-13 The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. + https://github.com/geneontology/go-ontology/issues/27054 organismal reproductive process Reactome:R-HSA-1474165 reproductive process in a multicellular organism @@ -22625,6 +22168,7 @@ Date accessed: 2015-04-13 An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. + https://github.com/geneontology/go-ontology/issues/20191 GO:0044112 GO:0044116 GO:0044117 @@ -22633,6 +22177,7 @@ Date accessed: 2015-04-13 GO:0044123 GO:0044125 Reactome:R-HSA-9635486 + Reactome:R-HSA-9640148 Reactome:R-HSA-9658195 interaction with host growth of symbiont in host @@ -22655,6 +22200,12 @@ Date accessed: 2015-04-13 Reactome:R-HSA-9635486 Infection with Mycobacterium tuberculosis + + + + Reactome:R-HSA-9640148 + Infection with Enterobacteria + @@ -22696,9 +22247,7 @@ Date accessed: 2015-04-13 measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. - - A data item label that denotes a unit of measure. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and @@ -22708,7 +22257,6 @@ of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot - http://purl.obolibrary.org/obo/obi.owl measurement unit label @@ -22784,19 +22332,13 @@ of this, different, term. - data item label datum label - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - An information content entity that is part of some data item and is used to partially define the denotation of that data item. http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO - datum label 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - http://purl.obolibrary.org/obo/obi.owl - data item label datum label @@ -22985,10 +22527,11 @@ Superclass was 'digital entity' + data entity data item Data items include counts of things, analyte concentrations, and statistical summaries. - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. @@ -23004,6 +22547,8 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data + data item + data entity data item @@ -23102,17 +22647,14 @@ Previous. An information content entity is a non-realizable information entity t 1 - scalar measurement datum 10 feet. 3 ml. A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot - http://purl.obolibrary.org/obo/obi.owl scalar measurement datum @@ -23489,6 +23031,7 @@ XML document; The instructions in a XSD file" PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 + data format specification @@ -23497,8 +23040,8 @@ XML document; The instructions in a XSD file" - - data set + + homogenous data collection Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. @@ -23506,9 +23049,9 @@ XML document; The instructions in a XSD file" 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert - OBI_0000042 + data set group:OBI - data set + homogenous data collection @@ -23615,7 +23158,6 @@ superclass was 'digial entity' person:Chris Stoeckert OBI_0000305 group:OBI - http://purl.obolibrary.org/obo/obi.owl measurement datum @@ -24869,7 +24411,6 @@ GO gene ontology - @@ -24893,7 +24434,7 @@ GO gene ontology - + A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. Person: Jie Zheng @@ -24924,7 +24465,6 @@ GO gene ontology - @@ -24970,7 +24510,6 @@ points together with a line. - @@ -24999,7 +24538,7 @@ points together with a line. - + @@ -25121,7 +24660,6 @@ points together with a line. - @@ -26182,7 +25720,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - @@ -26210,6 +25747,19 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta + + + + + the section of the document where the title appears + This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself. + Charles Tapley Hoyt + https://github.com/information-artifact-ontology/IAO/issues/286 + title section + + + + @@ -26354,6 +25904,21 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta + + + + + data collection + A data entity that consists of multiple data entities. + Sebastian Duesing + data set + https://github.com/information-artifact-ontology/IAO/issues/283 + https://github.com/obi-ontology/obi/issues/1877 + data collection + + + + @@ -26420,7 +25985,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - + @@ -26429,7 +25994,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - @@ -37777,7 +37341,6 @@ No imports planned process Injecting mice with a vaccine in order to test its efficacy - A process that realizes a plan which is the concretization of a plan specification. A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some @@ -37807,7 +37370,7 @@ No imports - + investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). @@ -37915,9 +37478,9 @@ for now. - + study design execution - a planned process that carries out a study design + a planned process that carries out a study design study design execution @@ -38238,42 +37801,6 @@ for now. - - - - - latitude coordinate measurement datum - - A measurement datum that is the measure of the latitude coordinate of a site. - Person: Chris Stoeckert, Jie Zheng - latitude - NIAID GSCID-BRC metadata working group - http://purl.obolibrary.org/obo/obi.owl - Specimen Collection Location - Latitude - NIAID GSCID-BRC - latitude coordinate measurement datum - - - - - - - - - longitude coordinate measurement datum - - A measurement datum that is the measure of the longitude coordinate of a site. - Person: Chris Stoeckert, Jie Zheng - longitude - NIAID GSCID-BRC metadata working group - http://purl.obolibrary.org/obo/obi.owl - Specimen Collection Location - Longitude - NIAID GSCID-BRC - longitude coordinate measurement datum - - - - @@ -38311,31 +37838,13 @@ for now. - - - scalar value specification - - A value specification that consists of two parts: a numeral and a unit label - PERSON:Bjoern Peters - http://purl.obolibrary.org/obo/obi.owl - scalar value specification - + - - - value specification - The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. - - An information content entity that specifies a value within a classification scheme or on a quantitative scale. - This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. - PERSON:Bjoern Peters - http://purl.obolibrary.org/obo/obi.owl - value specification - + @@ -38420,7 +37929,6 @@ https://www.doi.org/ A completely executed planned process that produces output data from input data. A data transformation is a process which produces output data from input data - A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone @@ -38557,6 +38065,7 @@ https://www.doi.org/ A matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. + A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design @@ -38714,7 +38223,9 @@ https://www.doi.org/ A process in which at least one bodily component of an organsim participates. + Albert Goldfain http://www.jbiomedsem.com/content/1/1/10 + creation date: 2009-06-23T11:53:49Z From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060 bodily process @@ -39354,7 +38865,7 @@ Amanda Hicks - + @@ -39374,15 +38885,16 @@ Amanda Hicks - + - A facility that is run by a school organization and is the bearer of a school function. + An educational facility that is run by a school organization and is the bearer of a school function. Mathias Brochhausen + school facility @@ -39586,13 +39098,6 @@ Amanda Hicks - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0000117 - - - size @@ -39725,23 +39230,6 @@ Amanda Hicks - - - - - A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0001323 - - - - MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area. - area - - - - @@ -39757,21 +39245,6 @@ Amanda Hicks - - - - - A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. - http://purl.obolibrary.org/obo/pato.owl - 2-D size - quality - PATO:0001709 - - 2-D extent - - - - @@ -40101,8 +39574,6 @@ np.average(range(1,11), weights=range(10,0,-1)) death UBERON:0000071 - - death stage @@ -40136,8 +39607,6 @@ np.average(range(1,11), weights=range(10,0,-1)) UBERON:0000105 - - life cycle stage @@ -40471,8 +39940,6 @@ np.average(range(1,11), weights=range(10,0,-1)) A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. UBERON:0035943 - - life cycle temporal boundary @@ -40501,6 +39968,7 @@ np.average(range(1,11), weights=range(10,0,-1)) length unit + A unit which is a standard measure of the distance between two points. length unit @@ -40512,6 +39980,7 @@ np.average(range(1,11), weights=range(10,0,-1)) mass unit + A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit @@ -40523,6 +39992,7 @@ np.average(range(1,11), weights=range(10,0,-1)) time unit + A unit which is a standard measure of the dimension in which events occur in sequence. unitOfTime @@ -40531,21 +40001,6 @@ np.average(range(1,11), weights=range(10,0,-1)) - - - - - A unit which is a standard measure of the amount of a 2-dimensional flat surface. - http://purl.obolibrary.org/obo/uo.owl - george gkoutos - unit.ontology - UO:0000047 - - area unit - - - - @@ -40762,17 +40217,6 @@ np.average(range(1,11), weights=range(10,0,-1)) - - - - - Amanda Hicks - e.g., the EU - supranational entity - - - - @@ -40806,13 +40250,8 @@ np.average(range(1,11), weights=range(10,0,-1)) - http://www.geneontology.org/formats/oboInOwl - - - Obsolete Class Obsolete Class - obsolete_class @@ -40863,7 +40302,6 @@ np.average(range(1,11), weights=range(10,0,-1)) - angular degree angular degree ° @@ -40871,32 +40309,6 @@ np.average(range(1,11), weights=range(10,0,-1)) - - - - - radian - A unit of measurement of planar angles where a full circle is 2π. Specifically the angle is the length of the arc subtended by the angle divided by the circumference of the circle. - Josh Hanna - William R. Hogan - Technically in the S.I. system it is a derived unit m•m^-1. - rad - radian - - - - - - - - - square mile - An area unit which is equal to the area enclosed by a square in a flat plane which is one mile on every side. - square mile - - - - @@ -41175,6 +40587,20 @@ np.average(range(1,11), weights=range(10,0,-1)) + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + @@ -41185,12 +40611,13 @@ np.average(range(1,11), weights=range(10,0,-1)) - + - - - "An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST] - square meter + + + 2026-04-04T19:54:38Z + + William R. Hogan @@ -41404,18 +40831,12 @@ This interpretation is *not* the same as an at-all-times relation - - - - + - - - @@ -41531,7 +40952,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -41541,51 +40962,8 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -41617,7 +40995,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -41627,51 +41005,8 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -41703,7 +41038,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -41713,51 +41048,8 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -41789,7 +41081,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -41799,51 +41091,8 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + diff --git a/apollo_sv.json b/apollo_sv.json index d9792de..59f3845 100644 --- a/apollo_sv.json +++ b/apollo_sv.json @@ -49,11 +49,70 @@ "val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)." }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2026-03-13" + "val" : "2026-07-19" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2026-03-13/apollo_sv.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2026-07-19/apollo_sv.json" }, "nodes" : [ { + "id" : "http://humanbehaviourchange.org/ontology/BCIO_006158", + "lbl" : "habitual behaviour", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An that results from a learnt stimulus-behaviour co-occurrence." + }, + "comments" : [ "A learnt stimulus-behaviour co-occurrence can lead to activation or execution of a habitual behaviour.\n\nHabitual behaviour can be an MoA or outcome depending on how 'habitual behaviour' is described in an intervention. The Behaviour Change-Intervention Ontology includes the class 'outcome behaviour' (definition: Human behavior that is an intervention outcome.), which would not be an MoA. When an intervention targets a habitual behaviour to achieve an outcome behaviour, the former qualifies as an MoA." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " \"Habit\" in the Theory of Interpersonal Behavior" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "\"Habits\" in the Motivation-Opportunities-Abilities" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "Published" + } ] + } + }, { + "id" : "http://humanbehaviourchange.org/ontology/BCIO_026022", + "lbl" : "educational facility", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A facility in which formal education is provided to a student population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "Published" + } ] + } + }, { + "id" : "http://humanbehaviourchange.org/ontology/BCIO_036000", + "lbl" : "individual human behaviour", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A bodily process of a human that involves co-ordinated contraction of striated muscles controlled by the brain." + }, + "comments" : [ " it is concerned with moving skeletal parts to which it is usually attached.' (https://www.collinsdictionary.com/dictionary/english/striped-muscle)", "The class human behaviour [BCIO:042000] has been made obsolete. If you want to refer to the behaviour of an individual, refer to individual human behaviour . If you want to refer to the behaviour of a group, refer to population behaviour.\n\nStriated muscles referred to in the definition do not ordinarily involve cardiac muscles.\n\nBehaviours are usually in response to an internal or external stimuli.\n\nEvery behaviour is associated with mental processes, but not every mental process is associated with behaviour. For instance, a verbal communication behaviour will involve mental processes to produce speech. However, mental processes associated with listening can occur without a person performing a behaviour.\n\n'behaviours' can involve a series of activities (e.g., more granular behaviours).\n\n'A 'striated muscle' can defined as 'a type of contractile tissue that is marked by transverse striations" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Also referred to in definitions as human behaviour or just behaviour." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "walks for 15 mins/day, never eats meat, attends school daily" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "Published" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "human behaviour" + }, { + "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", + "val" : "HumanBehavior" + } ] + } + }, { "id" : "http://purl.obolibrary.obo/obo/NCBITaxon_7160", "lbl" : "Aedes albopictus", "type" : "CLASS", @@ -6500,7 +6559,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402", - "lbl" : "individual human behavior", + "lbl" : "obsolete individual human behavior", "type" : "CLASS", "meta" : { "definition" : { @@ -6516,9 +6575,10 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An individual behavior of a human being." }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "HumanBehavior" - } ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://humanbehaviourchange.org/ontology/BCIO_036000" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000403", @@ -11416,6 +11476,131 @@ "val" : "Intent to have one's child vaccinated." } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000653", + "lbl" : "human-to-human communicability", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A communicability among human beings (homo sapiens)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "communicability among human beings" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "The ability of a pathogen to transmit from one human host to another human host." + }, { + "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", + "val" : "HumanToHumanCommunicability" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000654", + "lbl" : "historical scenario", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disease scenario that represents or reconstructs an outbreak or epidemic that actually occurred, usually constrained by observed data." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "historical infectious disease scenario date" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "John Levander" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-04-04T19:36:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000655", + "lbl" : "hypothetical scenario", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An infectious disease scenario that represents a possible, assumed, projected, or counterfactual outbreak or epidemic, and does not need to correspond to a specific observed event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "hypothetical infecctious disease scenario" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "John Levander" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-04-04T19:52:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000656", + "lbl" : "antibody administration control strategy", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ApolloDev/apollo-sv/issues/273" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Lucie Contamin" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-07-13T14:13:40Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000657", + "lbl" : "antibody administration census", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A population treatment census that is about one or more antibody administrations to organisms in a population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ApolloDev/apollo-sv/issues/273" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Lucie Contamin" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-07-13T13:52:47Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "lbl" : "epidemic simulator action specification", @@ -11575,10 +11760,28 @@ "val" : "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" + "val" : "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000004" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" + } ] + } + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/001-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11603,31 +11806,85 @@ "val" : "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" + "val" : "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000007" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" + "val" : "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/008-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" + "val" : "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/126-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" + "val" : "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/009-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" + "val" : "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/011-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " + "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/009-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " + "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/126-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " + "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/008-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " + "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/011-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11655,25 +11912,70 @@ "val" : "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." + "val" : "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000006" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." + "val" : "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000012" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" + "val" : "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/077-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" + "val" : "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/108-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" + "val" : "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/079-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " + "val" : "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/108-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " + "val" : "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/079-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11685,7 +11987,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" + "val" : "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/017-002" + } ] + } }, "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ], "basicPropertyValues" : [ { @@ -11726,19 +12034,49 @@ "val" : "the interior of your mouth" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" + "val" : "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/134-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" + "val" : "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/018-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " + "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/134-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " + "val" : "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/018-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " + "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/017-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11760,19 +12098,52 @@ "val" : "BFO 2 Reference: Spatial regions do not participate in processes." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." + "val" : "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000002" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" + "val" : "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/035-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" + "val" : "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/036-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " + "val" : "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/036-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " + "val" : "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/035-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11791,25 +12162,70 @@ "val" : "TemporalRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional" + "val" : "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000003" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])" + "val" : "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/100-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" + "val" : "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/101-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" + "val" : "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/119-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " + "val" : "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/119-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " + "val" : "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/101-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " + "val" : "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/100-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11834,10 +12250,22 @@ "val" : "the surface of a sphere-shaped part of space" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" + "val" : "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/039-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " + "val" : "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/039-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11865,37 +12293,97 @@ "val" : "the spatiotemporal region occupied by the development of a cancer tumor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" + "val" : "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/095-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" + "val" : "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/096-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" + "val" : "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/099-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" + "val" : "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/098-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every spatiotemporal region occupies_spatiotemporal_region itself." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" + "val" : "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/107-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " + "val" : "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/107-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " + "val" : "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/099-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " + "val" : "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/096-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " + "val" : "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/095-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " + "val" : "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/098-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11907,7 +12395,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" + "val" : "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/083-003" + } ] + } }, "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ], "basicPropertyValues" : [ { @@ -11942,7 +12436,13 @@ "val" : "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " + "val" : "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/083-003" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -11976,16 +12476,40 @@ "val" : "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" + "val" : "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/062-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" + "val" : "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/063-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " + "val" : "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/063-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " + "val" : "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/062-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12022,16 +12546,40 @@ "val" : "the role of this boundary to delineate where Utah and Colorado meet" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" + "val" : "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/058-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" + "val" : "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/060-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " + "val" : "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/060-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " + "val" : "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/058-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12050,10 +12598,22 @@ "val" : "ZeroDimensionalSpatialRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" + "val" : "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/037-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " + "val" : "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/037-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12090,16 +12650,40 @@ "val" : "the shape of your nostril" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" + "val" : "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/055-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" + "val" : "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/105-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " + "val" : "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/055-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " + "val" : "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/105-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12111,7 +12695,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" + "val" : "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/050-003" + } ] + } }, "comments" : [ "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." ], "basicPropertyValues" : [ { @@ -12155,10 +12745,25 @@ "val" : "the smell of this portion of mozzarella" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." + "val" : "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "per discussion with Barry Smith" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " + "val" : "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/050-003" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12204,10 +12809,22 @@ "val" : "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" + "val" : "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/061-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " + "val" : "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/061-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12253,10 +12870,22 @@ "val" : "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])" + "val" : "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/027-004" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] " + "val" : "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/027-004" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12278,10 +12907,22 @@ "val" : "an edge of a cube-shaped portion of space." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])" + "val" : "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/038-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " + "val" : "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/038-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12340,25 +12981,46 @@ "val" : "your collection of Meissen ceramic plates." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " + "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000011" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000301" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." + "val" : "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000300" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" + "val" : "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/025-004" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " + "val" : "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/025-004" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12383,10 +13045,22 @@ "val" : "a sphere-shaped region of space," }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" + "val" : "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/040-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " + "val" : "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/040-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12450,10 +13124,22 @@ "val" : "your left nostril (a fiat part – the opening – of your left nasal cavity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" + "val" : "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/034-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " + "val" : "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/034-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12520,7 +13206,13 @@ "val" : "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" + "val" : "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/024-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12532,7 +13224,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" + "val" : "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/074-001" + } ] + } }, "comments" : [ "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." ], "basicPropertyValues" : [ { @@ -12552,7 +13250,13 @@ "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " + "val" : "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/074-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12583,10 +13287,22 @@ "val" : "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" + "val" : "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/064-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " + "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/064-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12598,7 +13314,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])" + "val" : "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/084-001" + } ] + } }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", @@ -12611,13 +13333,31 @@ "val" : "the boundary between the 2nd and 3rd year of your life." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" + "val" : "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/085-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " + "val" : "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/085-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " + "val" : "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/084-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12642,10 +13382,22 @@ "val" : "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" + "val" : "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/103-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " + "val" : "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/103-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", "val" : "Interval" @@ -12718,22 +13470,58 @@ "val" : "Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" + "val" : "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/019-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" + "val" : "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/020-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" + "val" : "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/021-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " + "val" : "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/019-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " + "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/021-002" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " + "val" : "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/020-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12745,7 +13533,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])" + "val" : "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/029-001" + } ] + } }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", @@ -12761,13 +13555,25 @@ "val" : "BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions." + "val" : "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000008" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every continuant fiat boundary is located at some spatial region at every time at which it exists" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] " + "val" : "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/029-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12820,10 +13626,22 @@ "val" : "the median sulcus of your tongue" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])" + "val" : "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/032-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " + "val" : "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/032-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12835,7 +13653,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])" + "val" : "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/093-002" + } ] + } }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", @@ -12854,13 +13678,31 @@ "val" : "The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])" + "val" : "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/094-005" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] " + "val" : "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/094-005" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " + "val" : "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/093-002" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12872,7 +13714,13 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])" + "val" : "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/057-001" + } ] + } }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", @@ -12888,7 +13736,13 @@ "val" : "a marriage bond, an instance of requited love, an obligation between one person and another." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] " + "val" : "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/057-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12907,10 +13761,22 @@ "val" : "TwoDimensionalContinuantFiatBoundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])" + "val" : "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/033-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " + "val" : "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/033-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12938,13 +13804,37 @@ "val" : "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])" + "val" : "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/0000001" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "requested by Melanie Courtot" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://groups.google.com/d/msg/bfo-owl-devel/s9Uug5QmAws/ZDRnpiIi_TUJ" + } ] + } + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/031-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " + "val" : "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/031-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -12981,10 +13871,22 @@ "val" : "temporal instant." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" + "val" : "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/102-001" + } ] + } }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " + "val" : "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] ", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/102-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -13006,7 +13908,13 @@ "val" : "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])" + "val" : "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0010000", + "val" : "http://purl.obolibrary.org/obo/bfo/axiom/138-001" + } ] + } }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" @@ -13038,7 +13946,32 @@ }, { "id" : "http://purl.obolibrary.org/obo/COB_0000035", "lbl" : "completely executed planned process", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "completely executed planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/cob.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/COB_0000082", + "lbl" : "planned process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "planned process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/cob.owl" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/DOID_0060478", "lbl" : "Zika fever", @@ -13262,6 +14195,25 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William Hogan" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/DRON_00000031", + "lbl" : "drug administration", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "administration of a drug product to an organism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "William R. Hogan" } ] } }, { @@ -13282,6 +14234,9 @@ }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-5039-2052" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "http://orcid.org/0000-0002-9881-1017" } ] } }, { @@ -13616,53 +14571,6 @@ "val" : "pub_type" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000001", - "lbl" : "geopolitical entity", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii)" - }, - "comments" : [ "In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000002", - "lbl" : "obsolete group of governmental organizations", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on." - }, - "comments" : [ "taken over by GEO_0000000401" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "obsolete aggregate of governmental organizations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000003", - "lbl" : "nation", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A geopolitical entity that is self contained and recognizes no higher political authority than itself." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000004", "lbl" : "subnational entity", @@ -13716,80 +14624,6 @@ "val" : "William R. Hogan" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000007", - "lbl" : "group of major administrative subdivisions", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common." - }, - "comments" : [ "Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000008", - "lbl" : "group of dependencies", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." - }, - "comments" : [ "Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000334", - "lbl" : "subcontinental land mass", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000335", - "lbl" : "contiguous land mass", - "type" : "CLASS", - "meta" : { - "comments" : [ "per the definition of 'contiguous' of \"being in actual contact : touching along a boundary or at a point\", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island.\n\nAt some point, we need an 'adjacent to' relation if BFO doesn't provide it.\n\nOne question is whether this class encompasses fiat parts of islands." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contiguous continental land mass" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000337", - "lbl" : "aggregate of governmental organizations", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members.\n" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000357", - "lbl" : "contiguous island land mass", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A subcontinental land mass that is part of an island and includes part of the land surface of the island." - }, - "comments" : [ "It cannot be a part of the island, for example, that is below water." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000369", - "lbl" : "aggregate of contiguous land masses", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000370", "lbl" : "geographical entity", @@ -13856,39 +14690,6 @@ "val" : "Location" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000373", - "lbl" : "body of water", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000374", - "lbl" : "continent", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000375", - "lbl" : "land mass", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000376", - "lbl" : "island", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000377", - "lbl" : "aggregate of geographical entities", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An object aggregate of geographical entities" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000378", - "lbl" : "aggregate of geographical features", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000390", - "lbl" : "aggregate of islands", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000391", "lbl" : "geopoli organization", @@ -13999,98 +14800,6 @@ "val" : "Amanda Hicks" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000401", - "lbl" : "aggregate of geopolitical organizations", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000402", - "lbl" : "obsolete aggregate of dependencies", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." - }, - "comments" : [ "Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000403", - "lbl" : "obsolete aggregate of major administrative subdivisions", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common" - }, - "comments" : [ "Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000404", - "lbl" : "aggregate of sovereign states", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common" - }, - "comments" : [ "examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000787", - "lbl" : "geodetic coordinate measurement datum", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum." - }, - "comments" : [ "latitude and longitude are key subtypes" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geodetic coordinate measurement datum" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Josh Hanna" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000788", "lbl" : "geodetic datum", @@ -14114,16 +14823,6 @@ "val" : "Wikipedia: https://en.wikipedia.org/wiki/Geodetic_datum\n\nDate accessed: 2015-04-13" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000789", - "lbl" : "plane angle measurement unit label", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "planar angular measurement unit label" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000797", "lbl" : "de jure sovereign state", @@ -14250,6 +14949,9 @@ "val" : "Wikipedia:Biological_process" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/24968" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" }, { @@ -14295,7 +14997,13 @@ "val" : "virulence" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-162906" + "val" : "Reactome:R-HSA-162906", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "HIV Infection" + } ] + } }, { "val" : "Wikipedia:Viral_life_cycle" } ], @@ -14322,9 +15030,21 @@ "val" : "phosphokinase activity" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-6788855" + "val" : "Reactome:R-HSA-6788855", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "FN3KRP phosphorylates PsiAm, RibAm" + } ] + } }, { - "val" : "Reactome:R-HSA-6788867" + "val" : "Reactome:R-HSA-6788867", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "FN3K phosphorylates ketosamines" + } ] + } } ] } }, { @@ -14354,11 +15074,29 @@ "xrefs" : [ "GOC:bf", "GOC:jl" ] } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-162588" + "val" : "Reactome:R-HSA-162588", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Budding and maturation of HIV virion" + } ] + } }, { - "val" : "Reactome:R-HSA-168255" + "val" : "Reactome:R-HSA-168255", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Influenza Infection" + } ] + } }, { - "val" : "Reactome:R-HSA-9609646" + "val" : "Reactome:R-HSA-9609646", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "HCMV Infection" + } ] + } } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", @@ -14394,6 +15132,9 @@ "val" : "single-organism reproductive behavior" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/23491" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" }, { @@ -14431,6 +15172,9 @@ "val" : "Wikipedia:Sexual_reproduction" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22929" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -14453,6 +15197,9 @@ "val" : "Wikipedia:Asexual_reproduction" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22929" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -14475,6 +15222,9 @@ "val" : "Wikipedia:Reproduction" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27054" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" }, { @@ -14513,6 +15263,9 @@ "val" : "single-multicellular organism process" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27189" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" }, { @@ -14570,7 +15323,22 @@ "pred" : "hasRelatedSynonym", "val" : "symbiotic process" } ], + "xrefs" : [ { + "val" : "Reactome:R-HSA-9839923", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Dengue Virus Infection" + } ] + } + } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/14807" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/20191" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0043298" }, { @@ -14667,9 +15435,18 @@ "val" : "other organism invasion" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-173107" + "val" : "Reactome:R-HSA-173107", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Binding and entry of HIV virion" + } ] + } } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/18563" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/go.owl" }, { @@ -14725,9 +15502,18 @@ "val" : "interspecies interaction with other organisms" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-9824443" + "val" : "Reactome:R-HSA-9824443", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Parasitic Infection Pathways" + } ] + } } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/20191" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -14750,9 +15536,18 @@ "val" : "reproductive process in a multicellular organism" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-1474165" + "val" : "Reactome:R-HSA-1474165", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Reproduction" + } ] + } } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27054" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -14799,11 +15594,34 @@ "val" : "growth of symbiont in host vacuole" } ], "xrefs" : [ { - "val" : "Reactome:R-HSA-9635486" + "val" : "Reactome:R-HSA-9635486", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Infection with Mycobacterium tuberculosis" + } ] + } }, { - "val" : "Reactome:R-HSA-9658195" + "val" : "Reactome:R-HSA-9640148", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Infection with Enterobacteria" + } ] + } + }, { + "val" : "Reactome:R-HSA-9658195", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#label", + "val" : "Leishmania infection" + } ] + } } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/20191" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0044112" }, { @@ -14881,9 +15699,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of measurement unit labels are liters, inches, weight per volume." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -14899,9 +15714,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -15026,17 +15838,11 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An information content entity that is part of some data item and is used to partially define the denotation of that data item." + "val" : "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data item label" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "datum label" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" @@ -15046,15 +15852,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP: IAO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "datum label" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. \n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -15310,9 +16110,12 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." + "val" : "An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data entity" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data item" }, { @@ -15348,6 +16151,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "data item" } ] } }, { @@ -15465,12 +16271,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." + "val" : "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "scalar measurement datum" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "10 feet. 3 ml." }, { @@ -15488,9 +16291,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -16134,11 +16934,14 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000187" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/172" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000100", - "lbl" : "data set", + "lbl" : "homogenous data collection", "type" : "CLASS", "meta" : { "definition" : { @@ -16146,7 +16949,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data set" + "val" : "homogenous data collection" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." @@ -16166,8 +16969,8 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000042" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "data set" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" @@ -16328,9 +17131,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -19661,6 +20461,25 @@ "val" : "https://en.wikipedia.org/wiki/Extract,_transform,_load" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000651", + "lbl" : "title section", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "the section of the document where the title appears" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Charles Tapley Hoyt" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/286" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000701", "lbl" : "descriptive data section", @@ -19933,6 +20752,31 @@ "val" : "https://github.com/information-artifact-ontology/IAO/issues/259" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0001000", + "lbl" : "data collection", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A data entity that consists of multiple data entities." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "data collection" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Sebastian Duesing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "data set" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/283" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obi-ontology/obi/issues/1877" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020000", "lbl" : "identifier", @@ -32005,74 +32849,6 @@ "val" : "NIAID GSCID-BRC" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001620", - "lbl" : "latitude coordinate measurement datum", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A measurement datum that is the measure of the latitude coordinate of a site." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "latitude coordinate measurement datum" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Chris Stoeckert, Jie Zheng" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "latitude" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "NIAID GSCID-BRC metadata working group" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/OBI_0001886", - "val" : "Specimen Collection Location - Latitude" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "NIAID GSCID-BRC" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OBI_0001621", - "lbl" : "longitude coordinate measurement datum", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A measurement datum that is the measure of the longitude coordinate of a site." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "longitude coordinate measurement datum" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Chris Stoeckert, Jie Zheng" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "longitude" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "NIAID GSCID-BRC metadata working group" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/OBI_0001886", - "val" : "Specimen Collection Location - Longitude" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "NIAID GSCID-BRC" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001628", "lbl" : "investigation identifier", @@ -32140,54 +32916,10 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001931", - "lbl" : "scalar value specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A value specification that consists of two parts: a numeral and a unit label" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "scalar value specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001933", - "lbl" : "value specification", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An information content entity that specifies a value within a classification scheme or on a quantitative scale." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "value specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001958", "lbl" : "systematic review study design", @@ -32275,7 +33007,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A planned process that produces output data from input data." + "val" : "A data transformation is a process which produces output data from input data" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -32745,8 +33477,14 @@ }, "comments" : [ "From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Albert Goldfain" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.jbiomedsem.com/content/1/1/10" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "creation date: 2009-06-23T11:53:49Z" } ] } }, { @@ -33302,11 +34040,14 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A facility that is run by a school organization and is the bearer of a school function." + "val" : "An educational facility that is run by a school organization and is the bearer of a school function." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" } ] } }, { @@ -33455,21 +34196,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000117", - "lbl" : "size", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim", "http://purl.obolibrary.org/obo/pato#scalar_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000122", "lbl" : "length", @@ -33674,24 +34401,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001323", - "lbl" : "area", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent." - }, - "comments" : [ "MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area." ], - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim", "http://purl.obolibrary.org/obo/pato#mpath_slim", "http://purl.obolibrary.org/obo/pato#scalar_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001708", "lbl" : "1-D extent", @@ -33713,27 +34422,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001709", - "lbl" : "2-D extent", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#attribute_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "2-D size" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/pato.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001961", "lbl" : "in contact with", @@ -34228,7 +34916,7 @@ "val" : "End of the life of an organism.", "xrefs" : [ "XAO:0000437" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "death" @@ -34248,7 +34936,7 @@ "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "developmental stage" @@ -34619,7 +35307,7 @@ "val" : "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_subset", "http://purl.obolibrary.org/obo/uberon/core#mouse_subset", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ] } }, { "id" : "http://purl.obolibrary.org/obo/UO_0000000", @@ -34639,6 +35327,9 @@ "lbl" : "length unit", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A unit which is a standard measure of the distance between two points." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "length unit" @@ -34652,6 +35343,9 @@ "lbl" : "mass unit", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A unit which is a standard measure of the amount of matter/energy of a physical object." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "mass unit" @@ -34665,6 +35359,9 @@ "lbl" : "time unit", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A unit which is a standard measure of the dimension in which events occur in sequence." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "time unit" @@ -34679,26 +35376,6 @@ "val" : "unitOfTime" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/UO_0000047", - "lbl" : "area unit", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A unit which is a standard measure of the amount of a 2-dimensional flat surface." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uo#unit_group_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/uo.owl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "george gkoutos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "unit.ontology" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/UO_0000186", "lbl" : "dimensionless unit", @@ -34953,17 +35630,6 @@ } ], "deprecated" : true } - }, { - "id" : "http://purl.obolibrary.org/obo/geo.owl/GEO_000000399", - "lbl" : "supranational entity", - "type" : "CLASS", - "meta" : { - "comments" : [ "e.g., the EU" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - } ] - } }, { "id" : "http://purl.org/obo/owl/FBcv#FBcv_0000209", "lbl" : "news article", @@ -34994,17 +35660,8 @@ } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", - "lbl" : "obsolete_class", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://www.geneontology.org/formats/oboInOwl" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147487145" - } ] - } + "lbl" : "Obsolete Class", + "type" : "CLASS" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#Subset", "type" : "CLASS" @@ -35103,7 +35760,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -35447,53 +36104,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000083", - "lbl" : "occupies spatial region at some time", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "located-at-r_st" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "occupiesSpatialRegionAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: independent continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: spatial region" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { @@ -35505,60 +36115,12 @@ "id" : "http://purl.obolibrary.org/obo/BFO_0000110", "lbl" : "has continuant part at all times", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-has-part_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "hasContinuantPartAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000111", "lbl" : "has proper continuant part at all times", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-has-ppart_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "hasProperContinuantPartAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000113", "lbl" : "has material basis at all times", @@ -35690,32 +36252,6 @@ "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000123", - "lbl" : "has spatial occupant at some time", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "r-location-of_st" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000132", "lbl" : "part of occurrent", @@ -35809,33 +36345,8 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000137", - "lbl" : "proper part of continuant at all times", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001])" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-ppart-of_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "properContinuantPartOfAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000138", "lbl" : "proper part of occurrent", @@ -36083,93 +36594,8 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000177", - "lbl" : "part of continuant at all times", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-part-of_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", - "val" : "continuantPartOfAt" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mary’s arm continuant_part_of Mary in the time of her life prior to her operation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", - "val" : "if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", - "val" : "(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] " - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000181", "lbl" : "has proper temporal part", @@ -36198,93 +36624,37 @@ "type" : "PROPERTY", "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000187", - "lbl" : "has continuant part at all times that part exists", + "id" : "http://purl.obolibrary.org/obo/IAO_0000011", + "lbl" : "is directed towards", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)" + "val" : "A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality." }, + "comments" : [ "In the definition source, the relation is called 'is_about'. To avoid confusion with the existing \"is about\" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", - "val" : "c-has-part-object_at" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'." + "val" : "One of my mental representations is directed towards the Pacific Ocean." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "person: William Hogan" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://ceur-ws.org/Vol-1515/regular10.pdf" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/285" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000328", - "lbl" : "is in aggregate", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000329", - "lbl" : "is subordinate authority of", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2." - }, - "comments" : [ "\n'is subordinate authority of'\nDomain: governing organization\nRange: governing organization\nFormal properties: transitive, anti-symmetric, irreflexive\nNatural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000336", - "lbl" : "has jurisdiction in", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "comments" : [ "It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c.\n\nin other words, it is perfectly fine to say:\na disjoint b\nc has_jurisdiction_in a\nc has_jurisdiction_in b\n\notherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it \"United States territory\", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities.", "a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories.", "if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b." ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000039", "lbl" : "has measurement unit label", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "A relation between a value specification and its unit of measurement." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has measurement unit label" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000135", "lbl" : "obsolete_specifically denotes", @@ -36325,7 +36695,7 @@ "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "is_about is a (currently) primitive relation that relates an information artifact to an entity." + "val" : "A (currently) primitive relation that relates an information artifact to an entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -36342,9 +36712,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { @@ -36662,19 +37029,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000293", - "lbl" : "has_specified_input", + "lbl" : "has specified input", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The inverse property of is_specified_input_of" + "val" : "The inverse property of is specified input of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has_specified_input" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has_specified_input" + "val" : "has specified input" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "see is_input_of example_of_usage" @@ -36699,55 +37063,25 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000295", - "lbl" : "is_specified_input_of", + "lbl" : "is specified input of", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is_specified_input_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Bjoern Peters" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000299", - "lbl" : "has_specified_output", + "lbl" : "has specified output", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The inverse property of is_specified_output_of" + "val" : "The inverse property of is specified output of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has specified output" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has_specified_output" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has_specified_output" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -36766,9 +37100,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -36780,22 +37111,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000312", - "lbl" : "is_specified_output_of", + "lbl" : "is specified output of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." + "val" : "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is specified output of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is_specified_output_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is_specified_output_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -36808,9 +37133,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -36844,30 +37166,8 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001938", - "lbl" : "has value specification", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "A relation between an information content entity and a value specification that specifies its value." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has value specification" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: James A. Overton" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", "lbl" : "owns", @@ -37027,9 +37327,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "participates_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { @@ -37062,9 +37359,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" @@ -38364,7 +38658,11 @@ "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." }, "comments" : [ "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" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002305", @@ -38375,7 +38673,11 @@ "definition" : { "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002314", @@ -40009,19 +40311,7 @@ "id" : "http://purl.obolibrary.org/obo/IAO_0000004", "lbl" : "has measurement value", "type" : "PROPERTY", - "propertyType" : "DATA", - "meta" : { - "definition" : { - "val" : "A relation between a scalar measurement data item and a number that quantifies it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The range should probably not be restricted to \"float\". It makes sense to set it to \"real\". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/obi.owl" - } ] - } + "propertyType" : "DATA" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000404", "lbl" : "has x coordinate value", @@ -40055,37 +40345,6 @@ "val" : "angular degree" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000791", - "lbl" : "radian", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A unit of measurement of planar angles where a full circle is 2π. Specifically the angle is the length of the arc subtended by the angle divided by the circumference of the circle." - }, - "comments" : [ "Technically in the S.I. system it is a derived unit m•m^-1." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "radian" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Josh Hanna" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000796", - "lbl" : "square mile", - "type" : "INDIVIDUAL", - "meta" : { - "comments" : [ "An area unit which is equal to the area enclosed by a square in a flat plane which is one mile on every side." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "square mile" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", @@ -40489,6 +40748,28 @@ "val" : "https://orcid.org/0000-0002-7356-1779" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0001002", + "lbl" : "domain entity does not exist", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0002-4142-7153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/136" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "https://orcid.org/0000-0002-4142-7153" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UO_0000034", "lbl" : "week", @@ -40497,11 +40778,17 @@ "comments" : [ "\"A time unit which is equal to 7 days.\" [Wikipedia:Wikipedia]" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UO_0000080", - "lbl" : "square meter", + "id" : "https://orcid.org/0000-0002-9881-1017", + "lbl" : "William R. Hogan", "type" : "INDIVIDUAL", "meta" : { - "comments" : [ "\"An area unit which is equal to an area enclosed by a square with sides each 1 meter long.\" [NIST:NIST]" ] + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2026-04-04T19:54:38Z" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-9881-1017" + } ] } }, { "id" : "http://protege.stanford.edu/plugins/owl/protege#defaultLanguage", @@ -40659,109 +40946,9 @@ "val" : "VIVO-ISF" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000009", - "lbl" : "US State Two Digit Identifier", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000010", - "lbl" : "US State Two Letter Abbreviation", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000011", - "lbl" : "US State Ens Identifier", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000021", - "lbl" : "UN Numerical Code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000022", - "lbl" : "ISO 3166-1-alpha-3 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000023", - "lbl" : "ISO 3166-1-alpha-2 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000358", - "lbl" : "Proposed Apollo Location Code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000000359", - "lbl" : "ISO 3166-2 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035330", - "lbl" : "geonameid", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "integer id of record in geonames database" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonameid" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035331", - "lbl" : "admin1 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "fipscode (subject to change to iso code), see exceptions below, see file admin1Codes.txt for display names of this code; varchar(20)" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonames admin1 code" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035332", - "lbl" : "admin2 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "code for the second administrative division, a county in the US, see file admin2Codes.txt; varchar(80)" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonames admin2 code" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035333", - "lbl" : "admin3 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "code for third level administrative division, varchar(20)" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonames admin3 code" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GEO_000035334", - "lbl" : "admin4 code", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "code for fourth level administrative division, varchar(20)" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "geonames admin4 code" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000111", - "lbl" : "editor preferred term~editor preferred label", + "lbl" : "editor preferred term", "type" : "PROPERTY", "propertyType" : "ANNOTATION", "meta" : { @@ -40975,6 +41162,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { @@ -41061,22 +41251,46 @@ "definition" : { "val" : "An IRI or similar locator for a request or discussion of an ontology term." }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term.", "The 'tracker item' can associate a tracker with a specific ontology term." ], + "xrefs" : [ { + "val" : "IAO:0000233" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term tracker item" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "term tracker item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { @@ -41618,10 +41832,366 @@ "val" : "https://orcid.org/0000-0002-8688-6599" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0002001", + "lbl" : "preferred label for community", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A provenance property that denotes a synonym to be the preferred one for a specific community." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease \"A\" and another one \"B\" (but they are the same thing)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/185" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2025-06-02" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing abbreviations or initialisms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003001", + "lbl" : "ambiguous synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing ambiguous synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", + "lbl" : "dubious synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing dubious synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "lbl" : "layperson synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing layperson or colloquial synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", "type" : "PROPERTY", - "propertyType" : "ANNOTATION" + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing pluralization synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003005", + "lbl" : "UK spelling synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing UK spelling variants" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003006", + "lbl" : "misspelling", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for common misspellings" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/132" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003007", + "lbl" : "misnomer", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/133" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003008", + "lbl" : "previous name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for names that have been used as primary labels in the past." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/139" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-07-25" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003009", + "lbl" : "legal name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for the legal entity name" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/141" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-07-27" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003010", + "lbl" : "International Nonproprietary Name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "INN" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) \"paracetamol\". In some cases such as this one, the INN might be the same as the ontology's primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/149" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-09-30" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "lbl" : "latin term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing Latin term synonyms." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "nasopharynx (UBERON:0001728) has the latin name \"pars nasalis pharyngis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/146" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-1773-2692" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-10-12" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003012", + "lbl" : "acronym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/135" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-11-01" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003014", + "lbl" : "has ontology hierarchical property", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: ` a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/IAO/issues/292" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2025-09-17" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0004000", + "lbl" : "has symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A serial number such as \"12324X\"; a stop sign; a written proper name such as \"OBI" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/144" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6523-4866" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2024-03-25" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001900", "lbl" : "temporal interpretation", @@ -41795,18 +42365,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "lbl" : "eco subset", @@ -41848,10 +42406,6 @@ "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/uo#unit_group_slim", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/contributor", "type" : "PROPERTY", @@ -41945,6 +42499,14 @@ "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/created", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/description", "type" : "PROPERTY", @@ -42020,14 +42582,19 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-7356-1779" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2024-03-18" } ] } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "lbl" : "has_definition", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -42178,6 +42745,18 @@ } } ], "edges" : [ { + "sub" : "http://humanbehaviourchange.org/ontology/BCIO_006158", + "pred" : "is_a", + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" + }, { + "sub" : "http://humanbehaviourchange.org/ontology/BCIO_026022", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" + }, { + "sub" : "http://humanbehaviourchange.org/ontology/BCIO_036000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000060" + }, { "sub" : "http://purl.obolibrary.obo/obo/NCBITaxon_7160", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_53541" @@ -42209,10 +42788,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000009", "pred" : "is_a", @@ -42337,10 +42912,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -42589,10 +43160,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000089", "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000025" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000090", "pred" : "is_a", @@ -43948,7 +44515,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0007610" + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000403", "pred" : "is_a", @@ -44469,6 +45036,10 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000531", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532", + "pred" : "is_a", + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532", "pred" : "is_a", @@ -44528,7 +45099,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000546", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402" + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000547", "pred" : "is_a", @@ -44577,6 +45148,10 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000558", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000558", "pred" : "is_a", @@ -44776,7 +45351,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000601", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000402" + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_036000" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000602", "pred" : "is_a", @@ -45017,6 +45592,30 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000652", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000650" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000653", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IDO_0000623" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000654", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000184" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000655", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000184" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000656", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000194" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000657", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000187" + }, { + "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000657", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", + "obj" : "http://purl.obolibrary.org/obo/DRON_00000031" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000793", "pred" : "is_a", @@ -45033,10 +45632,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -45220,6 +45815,10 @@ }, { "sub" : "http://purl.obolibrary.org/obo/COB_0000035", "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/COB_0000082" + }, { + "sub" : "http://purl.obolibrary.org/obo/COB_0000082", + "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/DOID_0060478", @@ -45245,6 +45844,10 @@ "sub" : "http://purl.obolibrary.org/obo/DRON_00000005", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/DRON_00000074" + }, { + "sub" : "http://purl.obolibrary.org/obo/DRON_00000031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000090" }, { "sub" : "http://purl.obolibrary.org/obo/DRON_00000074", "pred" : "is_a", @@ -45313,26 +45916,10 @@ "sub" : "http://purl.obolibrary.org/obo/FBcv_0000787", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000001", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000003", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000004", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GEO_000000400" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000004", - "pred" : "http://purl.obolibrary.org/obo/GEO_000000329", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000396" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000005", "pred" : "is_a", @@ -45341,58 +45928,6 @@ "sub" : "http://purl.obolibrary.org/obo/GEO_000000006", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GEO_000000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000007", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000007", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000005" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000008", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000006" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000334", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000375" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000334", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000137", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000374" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000335", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000334" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000337", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000337", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000400" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000357", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000334" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000369", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000375" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000369", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000377" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000369", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000375" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000370", "pred" : "is_a", @@ -45405,46 +45940,6 @@ "sub" : "http://purl.obolibrary.org/obo/GEO_000000372", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GEO_000000370" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000373", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000372" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000374", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000375" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000375", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000372" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000376", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000334" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000377", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000377", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000370" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000378", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000377" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000378", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000371" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000390", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000369" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000390", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000376" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000391", "pred" : "is_a", @@ -45469,42 +45964,10 @@ "sub" : "http://purl.obolibrary.org/obo/GEO_000000400", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000401", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000401", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000391" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000402", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000403", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000404", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000337" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000404", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000075", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000396" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000787", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000109" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000788", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000789", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000797", "pred" : "is_a", @@ -45800,7 +46263,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000100", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" + "obj" : "http://purl.obolibrary.org/obo/IAO_0001000" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000101", "pred" : "is_a", @@ -46137,10 +46600,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000443", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000443", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000443", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46152,7 +46611,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000444", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000445", "pred" : "is_a", @@ -46161,10 +46620,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000572", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000572", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000572", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46181,10 +46636,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000574", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000574", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000574", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -46196,7 +46647,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000575", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000575", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46233,10 +46684,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000580", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000580", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000580", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46557,10 +47004,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000650", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000650", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000650", "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", @@ -46569,6 +47012,10 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000650", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0000651", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000314" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000701", "pred" : "is_a", @@ -46601,6 +47048,10 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000708", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000578" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0001000", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020000", "pred" : "is_a", @@ -46621,10 +47072,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/COB_0000035" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", @@ -49240,7 +49687,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000115", "pred" : "is_a", @@ -49260,7 +49707,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000471", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + "obj" : "http://purl.obolibrary.org/obo/COB_0000035" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000576", "pred" : "is_a", @@ -49321,14 +49768,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0001615", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000300" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001620", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000787" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001621", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000787" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0001628", "pred" : "is_a", @@ -49337,14 +49776,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0001629", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001931", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0001933" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001933", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0001958", "pred" : "is_a", @@ -49636,7 +50067,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" + "obj" : "http://humanbehaviourchange.org/ontology/BCIO_026022" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", @@ -49721,18 +50152,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001241", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001323", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001709" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001708", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001709", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0000117" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001961", "pred" : "is_a", @@ -49861,10 +50284,6 @@ "sub" : "http://purl.obolibrary.org/obo/UO_0000003", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/UO_0000047", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/UO_0000186", "pred" : "is_a", @@ -49905,10 +50324,6 @@ "sub" : "http://purl.obolibrary.org/obo/VO_0000590", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/geo.owl/GEO_000000399", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000400" }, { "sub" : "http://purl.org/obo/owl/FBcv#FBcv_0000209", "pred" : "is_a", @@ -49929,18 +50344,6 @@ "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000113", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000107" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000790", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000789" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000791", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000789" - }, { - "sub" : "http://purl.obolibrary.org/obo/GEO_000000796", - "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/UO_0000047" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000002", "pred" : "type", @@ -50021,14 +50424,18 @@ "sub" : "http://purl.obolibrary.org/obo/OMO_0001000", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMO_0001002", + "pred" : "type", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/UO_0000034", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/UO_0000003" }, { - "sub" : "http://purl.obolibrary.org/obo/UO_0000080", + "sub" : "https://orcid.org/0000-0002-9881-1017", "pred" : "type", - "obj" : "http://purl.obolibrary.org/obo/UO_0000047" + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000004", "pred" : "subPropertyOf", @@ -50085,10 +50492,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000075", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000110", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000111", "pred" : "subPropertyOf", @@ -50121,10 +50524,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000136", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000139" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000137", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000177" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000138", "pred" : "subPropertyOf", @@ -50145,10 +50544,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000156", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000177", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000181", "pred" : "subPropertyOf", @@ -50161,10 +50556,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000184", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000066" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000187", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000039", "pred" : "subPropertyOf", @@ -50173,10 +50564,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000135", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0000136", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000142", "pred" : "subPropertyOf", @@ -50229,10 +50616,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000293", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0000295", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000056" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000299", "pred" : "subPropertyOf", @@ -50249,10 +50632,6 @@ "sub" : "http://purl.obolibrary.org/obo/OBI_0000417", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/OBI_0001938", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", "pred" : "subPropertyOf", @@ -50277,14 +50656,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000053", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0000056", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0000057", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000079", "pred" : "subPropertyOf", @@ -50949,22 +51320,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000066", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000067" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000075", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/GEO_000000328" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000083", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000123" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000117", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000132" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000137", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000142", "pred" : "inverseOf", @@ -50985,6 +51344,10 @@ "sub" : "http://purl.obolibrary.org/obo/OBIB_0000732", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/OBIB_0000735" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000293", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000295" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000299", "pred" : "inverseOf", @@ -51119,7 +51482,7 @@ "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000009", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] @@ -51151,7 +51514,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032" @@ -51588,7 +51951,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0000100" @@ -51600,16 +51963,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000798" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GEO_000000004", - "genusIds" : [ "http://purl.obolibrary.org/obo/GEO_000000400" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/GEO_000000329", - "fillerId" : "http://purl.obolibrary.org/obo/GEO_000000396" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GEO_000000787", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000109" ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019098", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007610", "http://purl.obolibrary.org/obo/GO_0048609" ] @@ -51638,7 +51991,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020010", - "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020000" @@ -51792,7 +52145,7 @@ } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000312", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035", "http://purl.obolibrary.org/obo/OBI_0000011" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ], "allValuesFromEdges" : [ { "sub" : "http://purl.obolibrary.org/obo/IAO_0000013", "pred" : "http://purl.obolibrary.org/obo/OBI_0000312", @@ -51847,14 +52200,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000083", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000006" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000123", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000006" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000155", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -51871,14 +52216,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000185", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/GEO_000000329", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/GEO_000000400" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GEO_000000400" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/GEO_000000336", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/GEO_000000400" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/GEO_000000375" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000136", "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ] @@ -51911,10 +52248,10 @@ "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000582" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000293", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000299", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035", "http://purl.obolibrary.org/obo/OBI_0000011" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/COB_0000035" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], diff --git a/apollo_sv.obo b/apollo_sv.obo index 158170c..795e7b4 100644 --- a/apollo_sv.obo +++ b/apollo_sv.obo @@ -1,6 +1,5 @@ format-version: 1.2 -data-version: releases/2026-03-13 -subsetdef: attribute_slim "" +data-version: releases/2026-07-19 subsetdef: common_anatomy "" subsetdef: efo_slim "" subsetdef: gocheck_do_not_annotate "" @@ -24,16 +23,25 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: human_reference_atlas "" subsetdef: human_subset "" subsetdef: mouse_subset "" -subsetdef: mpath_slim "" subsetdef: pheno_slim "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" -subsetdef: scalar_slim "" subsetdef: uberon_slim "" -subsetdef: unit_group_slim "" subsetdef: upper_level "" subsetdef: vertebrate_core "" -synonymtypedef: OMO:0003004 "" +synonymtypedef: OMO:0003000 "abbreviation" +synonymtypedef: OMO:0003001 "ambiguous synonym" +synonymtypedef: OMO:0003002 "dubious synonym" +synonymtypedef: OMO:0003003 "layperson synonym" +synonymtypedef: OMO:0003004 "plural form" +synonymtypedef: OMO:0003005 "UK spelling synonym" +synonymtypedef: OMO:0003006 "misspelling" +synonymtypedef: OMO:0003007 "misnomer" +synonymtypedef: OMO:0003008 "previous name" +synonymtypedef: OMO:0003009 "legal name" +synonymtypedef: OMO:0003010 "International Nonproprietary Name" +synonymtypedef: OMO:0003011 "latin term" +synonymtypedef: OMO:0003012 "acronym" idspace: ace_lexicon http://attempto.ifi.uzh.ch/ace_lexicon# idspace: dc http://purl.org/dc/elements/1.1/ idspace: doap http://usefulinc.com/ns/doap# @@ -56,7 +64,7 @@ property_value: dc:contributor "Mike Wagner" xsd:string property_value: dc:contributor "Shawn T. Brown" xsd:string property_value: dc:contributor "William R. Hogan" xsd:string property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: owl:versionInfo "2026-03-13" xsd:string +property_value: owl:versionInfo "2026-07-19" xsd:string property_value: terms:contributor "https://orcid.org/0000-0002-9881-1017" xsd:anyURI property_value: terms:description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string @@ -134,7 +142,6 @@ id: APOLLO_SV:00000008 name: software development def: "A planned process that has specified output a software product and that involves the creation of source code." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Software_development" xsd:string @@ -327,7 +334,7 @@ id: APOLLO_SV:00000032 name: count def: "A measurement datum that is the output of counting." [] is_a: IAO:0000109 ! measurement datum -intersection_of: IAO:0000027 ! data item +intersection_of: IAO:0000027 ! data entity intersection_of: OBI:0000312 APOLLO_SV:00000033 ! is specified output of counting relationship: OBI:0000312 APOLLO_SV:00000033 ! is specified output of counting property_value: APOLLO_SV:0000040 "count" xsd:string @@ -339,8 +346,7 @@ id: APOLLO_SV:00000033 name: counting def: "The planned process of finding the number of elements in a finite set of objects." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -intersection_of: OBI:0000011 ! planned process +intersection_of: COB:0000035 ! completely executed planned process intersection_of: OBI:0000299 APOLLO_SV:00000032 ! has specified output count relationship: OBI:0000299 APOLLO_SV:00000032 ! has specified output count property_value: IAO:0000117 "Mathias Brochhausen" xsd:string @@ -599,7 +605,7 @@ def: "An action specification that specifies the length of the time steps interv comment: simulation time step value\nsimulation time step unit\nsimulation run length\n\nThe time step value and unit are specified using a scalar value specification. is_a: APOLLO_SV:00000793 ! epidemic simulator action specification relationship: IAO:0000136 APOLLO_SV:00000066 ! is about simulation of time step -relationship: OBI:0001938 OBI:0001931 ! has value specification scalar value specification +relationship: OBI:0001938 OBI:0001931 relationship: part_of APOLLO_SV:00000007 ! simulation software application property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "An action specification that specifies the length of the time steps interval assumed in a simulation." xsd:string @@ -738,7 +744,7 @@ property_value: IAO:0000600 "A control strategy dose schedule specifies the inte id: APOLLO_SV:00000085 name: age data in age brackets data set def: "A data set consisting of measurements of age organized in age brackets." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: IAO:0000111 "age structure data set" xsd:string property_value: IAO:0000600 "A data set consisting of measurements of age organized in age brackets." xsd:string @@ -782,7 +788,6 @@ property_value: IAO:0000600 "A vaccination efficacy that results from a vaccinat id: APOLLO_SV:00000090 name: vaccination efficacy study design execution def: "A study design execution that has as its specified output one or more measured vaccination efficacy data items" [] -is_a: COB:0000035 ! completely executed planned process is_a: OBI:0000471 ! study design execution intersection_of: OBI:0000471 ! study design execution intersection_of: has_part APOLLO_SV:00000142 ! vaccination @@ -1098,7 +1103,7 @@ property_value: IAO:0000600 "An event in the ecosystem that triggers the startin id: APOLLO_SV:00000131 name: reactive control strategy threshold def: "A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "reactiveControlMeasureThreshold" xsd:string property_value: IAO:0000600 "A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.\n\nThe event could be infection acquisition, vaccination, antiviral treatment, etc." xsd:string @@ -1127,7 +1132,7 @@ property_value: IAO:0000600 "Number of time steps it takes medical personnel to id: APOLLO_SV:00000135 name: ascertainment fraction comment: fraction of organisms (usually infected) that a surveillance system detects out of the total population -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "fractionInState" xsd:string property_value: IAO:0000600 "Fraction of all symptomatic individuals who will be ascertained" xsd:string @@ -1437,8 +1442,8 @@ name: antiviral treatment def: "A treatment with an antiviral drug." [] is_a: APOLLO_SV:00000318 ! drug treatment intersection_of: APOLLO_SV:00000318 ! drug treatment -intersection_of: OBI:0000293 CHEBI:36044 ! has_specified_input antiviral drug -relationship: OBI:0000293 CHEBI:36044 ! has_specified_input antiviral drug +intersection_of: OBI:0000293 CHEBI:36044 ! has specified input antiviral drug +relationship: OBI:0000293 CHEBI:36044 ! has specified input antiviral drug property_value: APOLLO_SV:0000040 "AntiviralTreatment" xsd:string property_value: IAO:0000600 "A treatment of a particular host with a particular antiviral drug with activity against a particular viral pathogen." xsd:string @@ -1540,7 +1545,7 @@ id: APOLLO_SV:00000184 name: infectious disease scenario def: "A dataset that represents at least one pathogen population (of a particular biological taxon) in one host population (of a particular biological taxon) in an ecosystem in a particular location at a particular point in time." [] comment: An infectious disease scenario contains counts of infections of a particular pathogen in a particular host in a particular ecosystem at a particular point in time, minimally. Agent-based ecosystems represent each host individually. \n\nThe infectious disease scenario typically also includes a lot of additional data about the ecosystem, including data about things like transmission probabililites, control measures, the immunity or other resistance status of host individuals, and so on. -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 APOLLO_SV:00000097 ! is about ecosystem property_value: APOLLO_SV:0000040 "InfectiousDiseaseScenario" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -1618,7 +1623,7 @@ is_obsolete: true id: APOLLO_SV:00000193 name: vaccination efficacy inferred def: "A data item inferring a vaccination efficacy based on epidemiological data." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "VaccinationEfficacyInferred" xsd:string property_value: IAO:0000600 "A data item inferring a vaccination efficacy based on epidemiological data." xsd:string @@ -1819,7 +1824,7 @@ property_value: IAO:0000600 "A probability distribution over a discrete random v id: APOLLO_SV:00000217 name: infection state data item def: "A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "infectionState" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen." xsd:string @@ -2031,7 +2036,7 @@ property_value: IAO:0000600 "A information content entity that specifies the dat id: APOLLO_SV:00000241 name: age range category def: "An information content entity specifying the upper and lower limit of a range of ages of continuants." [] -is_a: OBI:0001931 ! scalar value specification +is_a: OBI:0001931 property_value: APOLLO_SV:0000040 "AgeRangeCategoryDefinition" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000600 "An information content entity specifying the upper and lower limit of a range of ages of continuants." xsd:string @@ -2700,8 +2705,8 @@ name: drug treatment def: "A treatment with a drug product." [] is_a: OGMS:0000090 ! treatment intersection_of: OGMS:0000090 ! treatment -intersection_of: OBI:0000293 DRON:00000005 ! has_specified_input clinical drug product -relationship: OBI:0000293 DRON:00000005 ! has_specified_input clinical drug product +intersection_of: OBI:0000293 DRON:00000005 ! has specified input clinical drug product +relationship: OBI:0000293 DRON:00000005 ! has specified input clinical drug product property_value: APOLLO_SV:0000040 "DrugTreatment" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Treatment with a drug." xsd:string @@ -3427,7 +3432,7 @@ property_value: IAO:0000600 "A population survey that assesses the presence (plu id: APOLLO_SV:00000397 name: infection case list def: "A data set that is a collection of case records." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: APOLLO_SV:0000040 "CaseList" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3437,7 +3442,7 @@ property_value: IAO:0000600 "A data set that is a collection of case records." x id: APOLLO_SV:00000398 name: infection case record def: "A data set whose data items are about a host and its participation in an infection and potentially other activities occuring in the same time interval as the infection." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: APOLLO_SV:0000040 "CaseRecord" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3474,13 +3479,14 @@ property_value: IAO:0000600 "An individual behavior of a mosquito (organism of f [Term] id: APOLLO_SV:00000402 -name: individual human behavior +name: obsolete individual human behavior def: "An individual behavior of a human being." [] -is_a: GO:0007610 ! behavior -property_value: APOLLO_SV:0000040 "HumanBehavior" xsd:string +is_a: oboInOwl:ObsoleteClass ! Obsolete Class property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An individual behavior of a human being." xsd:string +is_obsolete: true +replaced_by: BCIO:036000 [Term] id: APOLLO_SV:00000403 @@ -3687,7 +3693,7 @@ property_value: IAO:0000600 "A process of change in fecundity of females in a mo id: APOLLO_SV:00000422 name: confidence interval def: "A data item that specifies both an interval estimate centered around some sample statistic, and the probability that the process/method of obtaining the interval estimate's range of values will generate an interval that contains some unobserved population parameter of interest." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3763,7 +3769,7 @@ property_value: IAO:0000600 "A name of a temporal region that is systematized ac id: APOLLO_SV:00000430 name: ring diameter in meters def: "A scalar value specification that gives the diameter in meters of the circular area around which all organisms in a population are living will receive a vaccination as part of a ring vaccination control measure." [] -is_a: OBI:0001931 ! scalar value specification +is_a: OBI:0001931 property_value: APOLLO_SV:0000040 "ringDiameterInMeters" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3783,7 +3789,7 @@ property_value: IAO:0000600 "An epidemic simulator actions specification that sp id: APOLLO_SV:00000432 name: minimum value def: "A data item that specifies the smallest numerical value in a data set of scalar measurement data items." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "minimumValue" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3793,7 +3799,7 @@ property_value: IAO:0000600 "A data item that specifies the smallest numerical v id: APOLLO_SV:00000433 name: maximum value def: "A data item that specifies the largest numerical value in a data set of scalar measurement data itmes." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "maximumValue" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3922,7 +3928,7 @@ property_value: IAO:0000600 "A rate measurement datum that specifies the percent id: APOLLO_SV:00000446 name: ratio of outdoor to indoor ovisites def: "A data item that specifies, as a ratio, the total count of oviposition sites located externally to all places in a geographic region relative to the total count of oviposition sites located internally to some place in that geographic region." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "ratioOfOutdoorToIndoorOvisites" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -3942,7 +3948,7 @@ property_value: IAO:0000600 "An information content entity that delimits an inte id: APOLLO_SV:00000448 name: standard deviation def: "A data item that specifies the dispersion of values around some parameter in a set of data, and whose values are standardized to express the same unit of measure as the parameter of interest." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "standardDeviation" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4164,7 +4170,7 @@ id: APOLLO_SV:00000470 name: probability def: "A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents." [] comment: The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'. -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "Probability" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4658,7 +4664,7 @@ id: APOLLO_SV:00000522 name: source code repository def: "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc." [] comment: Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection is_a: IAO:0000310 ! document relationship: has_part IAO:0000096 ! source code module property_value: IAO:0000111 "software source code version control repository" xsd:string @@ -4702,7 +4708,7 @@ id: APOLLO_SV:00000528 name: synthetic ecosystem data set def: "A data set that represents 1) one or more collections of organisms at some time and some geographical region; and optionally 2) the school facilities, workplace facilities, and health care facilities in that region." [] comment: The interactions between each organism as they move between these facilities may also be included in the data set. -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 APOLLO_SV:00000097 ! is about ecosystem property_value: APOLLO_SV:0000040 "SyntheticEcosystem" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -4732,7 +4738,7 @@ property_value: IAO:0000600 "A conditional probability whose value is dependent id: APOLLO_SV:00000531 name: epidemic threshold def: "A data item that specifies the number of susceptible organisms necessary for an epidemic to occur within a population." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4741,6 +4747,7 @@ id: APOLLO_SV:00000532 name: human travel def: "A geographical migration of an organism belonging to the species Homo sapiens." [] is_a: APOLLO_SV:00000480 ! geographical movement of organism +is_a: BCIO:036000 ! individual human behaviour property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4756,7 +4763,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000534 name: human mobility data item def: "A data item that is about one or more instances of human travel, and that specifies the geographical start location, geographical end location, and the geographical regions visited throughout the process." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4833,7 +4840,7 @@ property_value: IAO:0000600 "An objective specification whose endpoint is human id: APOLLO_SV:00000542 name: mortality data def: "A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 PCO:0000001 ! is about population property_value: IAO:0000111 "population mortality data set" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -4863,7 +4870,7 @@ property_value: IAO:0000600 "A planned process that is the realization of a dise id: APOLLO_SV:00000546 name: self-initiated travel avoidance behavior def: "Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition." [] -is_a: APOLLO_SV:00000402 ! individual human behavior +is_a: BCIO:036000 ! individual human behaviour property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition." xsd:string @@ -4872,7 +4879,7 @@ property_value: IAO:0000600 "Individual human behavior that involves either 1) r id: APOLLO_SV:00000547 name: social interaction data item def: "A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s)." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s)." xsd:string @@ -4935,7 +4942,7 @@ property_value: IAO:0000600 "A Susceptible-Infected-Resistant model that represe id: APOLLO_SV:00000554 name: disease surveillance data def: "A data set that is about some disease surveillance." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: OBI:0000312 APOLLO_SV:00000545 ! is specified output of disease surveillance property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4975,6 +4982,7 @@ property_value: IAO:0000118 "infectious disease forecasting software application id: APOLLO_SV:00000558 name: case series def: "An investigation that realizes the concretization of some disease state design and that has as an occurrent part some population survey that\nhas specified input some case definition." [] +is_a: OBI:0000011 ! planned process is_a: OBI:0000066 ! investigation property_value: APOLLO_SV:0000040 "CaseSeries" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string @@ -4985,7 +4993,7 @@ property_value: IAO:0000600 "An investigation following a disease state study de id: APOLLO_SV:00000559 name: case series data set def: "A data set that is the output of a case series investigation." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: OBI:0000312 APOLLO_SV:00000558 ! is specified output of case series property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -4995,7 +5003,7 @@ property_value: IAO:0000600 "A data set that is the output of a case series inve id: APOLLO_SV:00000560 name: epidemic data set def: "A data set about an instance of an epidemic." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 APOLLO_SV:00000298 ! is about epidemic property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5047,7 +5055,7 @@ id: APOLLO_SV:00000566 name: data parsing def: "A data transformation that has a dataset, encoded in a particular data format specification, as input and extracts certain elements or parts of the dataset, typically into the volatile memory of a computer." [] is_a: OBI:0200000 ! data transformation -relationship: OBI:0000293 IAO:0000100 ! has_specified_input data set +relationship: OBI:0000293 IAO:0000100 ! has specified input homogenous data collection property_value: IAO:0000111 "data parsing process" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "data reading process" xsd:string @@ -5067,7 +5075,7 @@ property_value: IAO:0000118 "software for creating a synthetic ecosystem dataset id: APOLLO_SV:00000568 name: total fatal disease cases def: "A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "totalFatalCaseCount" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5089,7 +5097,7 @@ id: APOLLO_SV:00000570 name: employment status data item def: "A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions." [] comment: If an individual is a member of the labor force, the criteria that this status is selected from includes whether they are in the armed forces, employed and working, employed but absent from work for a week, and unemployed. The criteria for those not in the labor force includes whether the individual is a houseworker, suffering from a physical impairment that prevents them from working, in school, or other miscellaneous reasons. -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "employmentStatus" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5136,7 +5144,7 @@ property_value: IAO:0000118 "influenza-like illness" xsd:string id: APOLLO_SV:00000575 name: epidemic start week def: "A scalar value specification whose measurement unit label is 'week' and that is part of the first predicted data item that is greater than the epidemic threshold set for that data item." [] -is_a: OBI:0001931 ! scalar value specification +is_a: OBI:0001931 property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5145,7 +5153,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000576 name: epidemic peak week def: "A scalar value specification whose measurement unit label is 'week', and that is part of the epidemic peak intensity." [] -is_a: OBI:0001931 ! scalar value specification +is_a: OBI:0001931 property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5262,8 +5270,8 @@ name: website with data comment: This class was created for use case for MIDAS Digital Repository to index websites that have useful data in them, albeit rarely as machine-interpretable, downloadable datasets. Much of the data are locked in PDF or other text-based formats. is_a: FBcv:0000667 ! website intersection_of: FBcv:0000667 ! website -intersection_of: BFO:0000111 IAO:0000027 ! has proper continuant part at all times data item -relationship: BFO:0000111 IAO:0000027 ! has proper continuant part at all times data item +intersection_of: BFO:0000111 IAO:0000027 ! has proper continuant part at all times data entity +relationship: BFO:0000111 IAO:0000027 ! has proper continuant part at all times data entity property_value: IAO:0000111 "website that has data as a part" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5271,7 +5279,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000591 name: climate data set def: "A data set that is an aggregate of data items that are about an environmental system process (e.g., hydrological precipitation) or a participant in an environmental system process." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: IAO:0000111 "climate data set" xsd:string property_value: IAO:0000117 "Matt Diller" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5289,7 +5297,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000593 name: abiotic ecosystem data set def: "A data set that is about some abiotic ecosystem or abiotic ecosystem element." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: IAO:0000111 "abiotic ecosystem data set" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "abiotic ecosystem dataset" xsd:string @@ -5354,8 +5362,8 @@ id: APOLLO_SV:00000599 name: infection acquisition dataset def: "A dataset that is about infectious disease acquisitions at particular times and particular places." [] comment: The dataset may include sites (e.g. types of facilities, rooms), events (e.g., church service whether in or outdoors), dates, times, geographical regions, etc. in which the sites/events are located, and so on. -is_a: IAO:0000100 ! data set -intersection_of: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection +intersection_of: IAO:0000100 ! homogenous data collection intersection_of: IAO:0000136 APOLLO_SV:00000115 ! is about infection acquisition relationship: IAO:0000136 APOLLO_SV:00000115 ! is about infection acquisition property_value: dc:creator http://orcid.org/0000-0002-9881-1017 @@ -5369,7 +5377,7 @@ id: APOLLO_SV:00000600 name: hospital stay dataset def: "A dataset that is about two or more hospital stays involving two or more patients." [] comment: The dataset may be limited to stays in one hospital, but hospital discharge datasets as compiled by state departments of health typically contain stays from multiple hospitals (typically every hospital) in the geographical region over which they have jurisdiction -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: dc:creator http://orcid.org/0000-0002-9881-1017 property_value: dc:date "2021-03-16T16:20:48Z" xsd:dateTime property_value: IAO:0000111 "dataset about hospital stays" xsd:string @@ -5382,7 +5390,7 @@ property_value: IAO:0000118 "hospitalization dataset" xsd:string id: APOLLO_SV:00000601 name: human daily movement def: "An individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time." [] -is_a: APOLLO_SV:00000402 ! individual human behavior +is_a: BCIO:036000 ! individual human behaviour property_value: dc:creator http://orcid.org/0000-0002-9881-1017 property_value: dc:date "2021-03-16T16:29:53Z" xsd:dateTime property_value: IAO:0000111 "human daily movement behavior" xsd:string @@ -5392,8 +5400,8 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000602 name: human daily movement data set def: "A data set that is about the human daily movement behavior of the individual huamns in a given population." [] -is_a: IAO:0000100 ! data set -intersection_of: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection +intersection_of: IAO:0000100 ! homogenous data collection intersection_of: IAO:0000136 APOLLO_SV:00000601 ! is about human daily movement relationship: IAO:0000136 APOLLO_SV:00000601 ! is about human daily movement property_value: dc:creator http://orcid.org/0000-0002-9881-1017 @@ -5406,8 +5414,8 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000603 name: potentially infectious contact data set def: "A data set that is about one or more potentially infectious contact processes in a population of host organisms." [] -is_a: IAO:0000100 ! data set -intersection_of: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection +intersection_of: IAO:0000100 ! homogenous data collection intersection_of: IAO:0000136 APOLLO_SV:00000405 ! is about potentially infectious contacting relationship: IAO:0000136 APOLLO_SV:00000405 ! is about potentially infectious contacting property_value: dc:creator http://orcid.org/0000-0002-9881-1017 @@ -5536,7 +5544,7 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string id: APOLLO_SV:00000614 name: weather data set def: "A data set about the Earth's atmospheric weather" [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection property_value: dc:date "2022-09-18T18:34:00" xsd:string property_value: IAO:0000111 "data set about Earth's atmospheric weather" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -5859,6 +5867,62 @@ is_a: APOLLO_SV:00000650 ! intent to have a ward vaccinated property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "Intent to have one's child vaccinated." xsd:string +[Term] +id: APOLLO_SV:00000653 +name: human-to-human communicability +def: "A communicability among human beings (homo sapiens)." [] +is_a: IDO:0000623 ! communicability +property_value: APOLLO_SV:0000040 "HumanToHumanCommunicability" xsd:string +property_value: IAO:0000111 "communicability among human beings" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000600 "The ability of a pathogen to transmit from one human host to another human host." xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 + +[Term] +id: APOLLO_SV:00000654 +name: historical scenario +def: "An infectious disease scenario that represents or reconstructs an outbreak or epidemic that actually occurred, usually constrained by observed data." [] +is_a: APOLLO_SV:00000184 ! infectious disease scenario +property_value: dc:contributor "John Levander" xsd:string +property_value: IAO:0000111 "historical infectious disease scenario date" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 +property_value: terms:created "2026-04-04T19:36:00Z" xsd:dateTime + +[Term] +id: APOLLO_SV:00000655 +name: hypothetical scenario +def: "An infectious disease scenario that represents a possible, assumed, projected, or counterfactual outbreak or epidemic, and does not need to correspond to a specific observed event." [] +is_a: APOLLO_SV:00000184 ! infectious disease scenario +property_value: dc:contributor "John Levander" xsd:string +property_value: IAO:0000111 "hypothetical infecctious disease scenario" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 +property_value: terms:created "2026-04-04T19:52:04Z" xsd:dateTime + +[Term] +id: APOLLO_SV:00000656 +name: antibody administration control strategy +def: "An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process." [] +is_a: APOLLO_SV:00000194 ! individual treatment control strategy +property_value: dc:contributor "Lucie Contamin" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: term_tracker_item https://github.com/ApolloDev/apollo-sv/issues/273 +property_value: terms:created "2026-07-13T14:13:40Z" xsd:dateTime +property_value: terms:creator https://orcid.org/0000-0002-9881-1017 + +[Term] +id: APOLLO_SV:00000657 +name: antibody administration census +def: "A population treatment census that is about one or more antibody administrations to organisms in a population." [] +is_a: APOLLO_SV:00000187 ! population treatment census +relationship: IAO:0000136 DRON:00000031 ! is about drug administration +property_value: dc:contributor "Lucie Contamin" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: term_tracker_item https://github.com/ApolloDev/apollo-sv/issues/273 +property_value: terms:created "2026-07-13T13:52:47Z" xsd:dateTime +property_value: terms:creator https://orcid.org/0000-0002-9881-1017 + [Term] id: APOLLO_SV:00000793 name: epidemic simulator action specification @@ -5885,10 +5949,9 @@ id: APOLLO_SV:00000796 name: dataset creating def: "A planned process that has a data set as its specified output." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -intersection_of: OBI:0000011 ! planned process -intersection_of: OBI:0000299 IAO:0000100 ! has specified output data set -relationship: OBI:0000299 IAO:0000100 ! has specified output data set +intersection_of: COB:0000035 ! completely executed planned process +intersection_of: OBI:0000299 IAO:0000100 ! has specified output homogenous data collection +relationship: OBI:0000299 IAO:0000100 ! has specified output homogenous data collection property_value: IAO:0000111 "creating a data set" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "data set creation" xsd:string @@ -5967,6 +6030,35 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "The sensitivity of the process or system that detects organisms that have undergone a particular treatment" xsd:string is_obsolete: true +[Term] +id: BCIO:006158 +name: habitual behaviour +def: "An that results from a learnt stimulus-behaviour co-occurrence." [] +comment: A learnt stimulus-behaviour co-occurrence can lead to activation or execution of a habitual behaviour.\n\nHabitual behaviour can be an MoA or outcome depending on how 'habitual behaviour' is described in an intervention. The Behaviour Change-Intervention Ontology includes the class 'outcome behaviour' (definition: Human behavior that is an intervention outcome.), which would not be an MoA. When an intervention targets a habitual behaviour to achieve an outcome behaviour, the former qualifies as an MoA. +is_a: BCIO:036000 ! individual human behaviour +property_value: IAO:0000112 " \"Habit\" in the Theory of Interpersonal Behavior" xsd:string +property_value: IAO:0000112 "\"Habits\" in the Motivation-Opportunities-Abilities" xsd:string +property_value: IAO:0000114 "Published" xsd:string + +[Term] +id: BCIO:026022 +name: educational facility +def: "A facility in which formal education is provided to a student population." [] +is_a: OMRSE:00000062 ! facility +property_value: IAO:0000114 "Published" xsd:string + +[Term] +id: BCIO:036000 +name: individual human behaviour +def: "A of a human that involves co-ordinated contraction of striated muscles controlled by the brain." [] +comment: it is concerned with moving skeletal parts to which it is usually attached.' (https://www.collinsdictionary.com/dictionary/english/striped-muscle) +is_a: OGMS:0000060 ! bodily process +property_value: APOLLO_SV:0000040 "HumanBehavior" xsd:string +property_value: IAO:0000112 "Also referred to in definitions as human behaviour or just behaviour." xsd:string +property_value: IAO:0000112 "walks for 15 mins/day, never eats meat, attends school daily" xsd:string +property_value: IAO:0000114 "Published" xsd:string +property_value: IAO:0000118 "human behaviour" xsd:string + [Term] id: BFO:0000001 name: entity @@ -6303,9 +6395,7 @@ property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:stri property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011", IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} @@ -6597,8 +6687,18 @@ property_value: IAO:0000116 "Includes virus - we will later have a class for cel [Term] id: COB:0000035 name: completely executed planned process -is_a: BFO:0000015 ! process +is_a: COB:0000082 ! planned process disjoint_from: GO:0008150 ! biological_process +property_value: IAO:0000111 "completely executed planned process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/cob.owl + +[Term] +id: COB:0000082 +name: planned process +def: "A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification." [] +is_a: BFO:0000015 ! process +property_value: IAO:0000111 "planned process" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/cob.owl [Term] id: DOID:0060478 @@ -6703,6 +6803,15 @@ def: "A drug product that is bearer of a clinical drug role." [] comment: We changed the label to 'clinical drug product' because it was clear that the part of the definition re: bearer of a "clinical drug role" made it such. Other drugs don't have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf "drug product", which also required changing the definition here. is_a: DRON:00000074 ! drug product property_value: IAO:0000117 "William Hogan" xsd:string +property_value: terms:creator "https://orcid.org/0000-0002-9881-1017" xsd:anyURI + +[Term] +id: DRON:00000031 +name: drug administration +def: "A treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism." [] +is_a: OGMS:0000090 ! treatment +property_value: IAO:0000111 "administration of a drug product to an organism" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] id: DRON:00000074 @@ -6713,12 +6822,13 @@ is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-6378-1703 property_value: terms:contributor https://orcid.org/0000-0002-5039-2052 +property_value: terms:creator "http://orcid.org/0000-0002-9881-1017" xsd:string [Term] id: EFO:0004600 name: genomic data def: "Genomic data is data about the genomes of an organism." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: IAO:0000136 OBI:0100026 ! is about organism property_value: IAO:0000117 "James Malone" xsd:string @@ -6888,41 +6998,11 @@ subset: camcur is_a: IAO:0000310 ! document property_value: IAO:0000412 "http://purl.org/obo/owl/flybase_vocab" xsd:string -[Term] -id: GEO:000000001 -name: geopolitical entity -def: "An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii)" [] -comment: In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions. -is_a: oboInOwl:ObsoleteClass ! Obsolete Class -property_value: IAO:0000117 "William R. Hogan" xsd:string -is_obsolete: true - -[Term] -id: GEO:000000002 -name: obsolete group of governmental organizations -def: "An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on." [] -comment: taken over by GEO_0000000401 -is_a: BFO:0000004 ! independent continuant -property_value: IAO:0000111 "obsolete aggregate of governmental organizations" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -is_obsolete: true - -[Term] -id: GEO:000000003 -name: nation -def: "A geopolitical entity that is self contained and recognizes no higher political authority than itself." [] -is_a: oboInOwl:ObsoleteClass ! Obsolete Class -property_value: IAO:0000117 "William R. Hogan" xsd:string -is_obsolete: true - [Term] id: GEO:000000004 name: subnational entity def: "a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority" [] is_a: GEO:000000400 ! governmental organization -intersection_of: GEO:000000400 ! governmental organization -intersection_of: GEO:000000329 GEO:000000396 ! is subordinate authority of sovereign state -relationship: GEO:000000329 GEO:000000396 ! is subordinate authority of sovereign state property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -6945,60 +7025,6 @@ is_a: GEO:000000004 ! subnational entity property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string -[Term] -id: GEO:000000007 -name: aggregate of major administrative subdivisions -def: "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common." [] -comment: Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. -is_a: GEO:000000337 ! aggregate of governmental organizations -relationship: BFO:0000075 GEO:000000005 ! is aggregate of major administrative subdivision -property_value: IAO:0000117 "Amanda Hicks" xsd:string - -[Term] -id: GEO:000000008 -name: aggregate of dependencies -def: "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." [] -comment: Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. -is_a: GEO:000000337 ! aggregate of governmental organizations -relationship: BFO:0000075 GEO:000000006 ! is aggregate of geopolitical dependency -property_value: IAO:0000117 "Amanda Hicks" xsd:string - -[Term] -id: GEO:000000334 -name: subcontinental land mass -is_a: GEO:000000375 ! land mass -relationship: BFO:0000137 GEO:000000374 ! proper part of continuant at all times continent - -[Term] -id: GEO:000000335 -name: contiguous land mass -comment: per the definition of 'contiguous' of "being in actual contact : touching along a boundary or at a point", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island.\n\nAt some point, we need an 'adjacent to' relation if BFO doesn't provide it.\n\nOne question is whether this class encompasses fiat parts of islands. -is_a: GEO:000000334 ! subcontinental land mass -property_value: IAO:0000118 "contiguous continental land mass" xsd:string - -[Term] -id: GEO:000000337 -name: aggregate of governmental organizations -def: "An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members.\n" [] -is_a: BFO:0000004 ! independent continuant -relationship: BFO:0000075 GEO:000000400 ! is aggregate of governmental organization -property_value: IAO:0000117 "William R. Hogan" xsd:string - -[Term] -id: GEO:000000357 -name: contiguous island land mass -def: "A subcontinental land mass that is part of an island and includes part of the land surface of the island." [] -comment: It cannot be a part of the island, for example, that is below water. -is_a: GEO:000000334 ! subcontinental land mass -property_value: IAO:0000117 "William R. Hogan" xsd:string - -[Term] -id: GEO:000000369 -name: aggregate of contiguous land masses -is_a: GEO:000000375 ! land mass -is_a: GEO:000000377 ! aggregate of geographical entities -relationship: BFO:0000075 GEO:000000375 ! is aggregate of land mass - [Term] id: GEO:000000370 name: geographical entity @@ -7030,45 +7056,6 @@ property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers." xsd:string -[Term] -id: GEO:000000373 -name: body of water -is_a: GEO:000000372 ! geographical region - -[Term] -id: GEO:000000374 -name: continent -is_a: GEO:000000375 ! land mass - -[Term] -id: GEO:000000375 -name: land mass -is_a: GEO:000000372 ! geographical region - -[Term] -id: GEO:000000376 -name: island -is_a: GEO:000000334 ! subcontinental land mass - -[Term] -id: GEO:000000377 -name: aggregate of geographical entities -def: "An object aggregate of geographical entities" [] -is_a: BFO:0000027 ! object_aggregate -relationship: BFO:0000075 GEO:000000370 ! is aggregate of geographical entity - -[Term] -id: GEO:000000378 -name: aggregate of geographical features -is_a: GEO:000000377 ! aggregate of geographical entities -relationship: BFO:0000075 GEO:000000371 ! is aggregate of geographical feature - -[Term] -id: GEO:000000390 -name: aggregate of islands -is_a: GEO:000000369 ! aggregate of contiguous land masses -relationship: BFO:0000075 GEO:000000376 ! is aggregate of island - [Term] id: GEO:000000391 name: geopoli organization @@ -7117,13 +7104,6 @@ property_value: IAO:0000118 "nation" xsd:string property_value: IAO:0000118 "nation state" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Sovereign_state" xsd:string -[Term] -id: GEO:000000399 -name: supranational entity -comment: e.g., the EU -is_a: GEO:000000400 ! governmental organization -property_value: IAO:0000117 "Amanda Hicks" xsd:string - [Term] id: GEO:000000400 name: governmental organization @@ -7132,56 +7112,6 @@ comment: IMPORTANT: The label "geopolitical organization" was previously used fo is_a: OBI:0000245 ! organization property_value: IAO:0000117 "Amanda Hicks" xsd:string -[Term] -id: GEO:000000401 -name: aggregate of geopolitical organizations -def: "An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common" [] -is_a: BFO:0000004 ! independent continuant -relationship: BFO:0000075 GEO:000000391 ! is aggregate of geopoli organization -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000117 "William R. Hogan\n" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: GEO:000000402 -name: obsolete aggregate of dependencies -def: "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common." [] -comment: Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. -is_a: GEO:000000337 ! aggregate of governmental organizations -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string -is_obsolete: true - -[Term] -id: GEO:000000403 -name: obsolete aggregate of major administrative subdivisions -def: "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common" [] -comment: Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. -is_a: GEO:000000337 ! aggregate of governmental organizations -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string -is_obsolete: true - -[Term] -id: GEO:000000404 -name: aggregate of sovereign states -def: "An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common" [] -comment: examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc. -is_a: GEO:000000337 ! aggregate of governmental organizations -relationship: BFO:0000075 GEO:000000396 ! is aggregate of sovereign state -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: GEO:000000787 -name: geodetic coordinate measurement datum -def: "A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum." [] -comment: latitude and longitude are key subtypes -is_a: IAO:0000109 ! measurement datum -property_value: IAO:0000111 "geodetic coordinate measurement datum" xsd:string -property_value: IAO:0000117 "Josh Hanna" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string - [Term] id: GEO:000000788 name: geodetic datum @@ -7193,12 +7123,6 @@ property_value: IAO:0000117 "Josh Hanna" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000119 "Wikipedia: https://en.wikipedia.org/wiki/Geodetic_datum\n\nDate accessed: 2015-04-13" xsd:string -[Term] -id: GEO:000000789 -name: plane angle measurement unit label -is_a: IAO:0000003 ! measurement unit label -property_value: IAO:0000111 "planar angular measurement unit label" xsd:string - [Term] id: GEO:000000797 name: de jure sovereign state @@ -7270,6 +7194,7 @@ synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI created_by: jl creation_date: 2012-09-19T15:05:24Z @@ -7335,6 +7260,7 @@ is_a: GO:0048609 ! multicellular organismal reproductive process intersection_of: GO:0007610 ! behavior intersection_of: GO:0048609 ! multicellular organismal reproductive process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23491" xsd:anyURI created_by: jl creation_date: 2012-09-19T16:01:37Z @@ -7348,6 +7274,7 @@ subset: gocheck_do_not_annotate xref: Wikipedia:Sexual_reproduction is_a: APOLLO_SV:00000651 ! reproduction is_a: GO:0022414 ! reproductive process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22929" xsd:anyURI [Term] id: GO:0019954 @@ -7358,6 +7285,7 @@ synonym: "parthenogenesis" RELATED [Wikipedia:Parthenogenesis] xref: Wikipedia:Asexual_reproduction is_a: APOLLO_SV:00000651 ! reproduction is_a: GO:0022414 ! reproductive process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22929" xsd:anyURI [Term] id: GO:0022414 @@ -7378,6 +7306,7 @@ subset: goslim_plant_ribbon synonym: "single organism reproductive process" RELATED [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI created_by: jl creation_date: 2012-09-19T15:56:06Z @@ -7394,6 +7323,7 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -7417,7 +7347,10 @@ synonym: "symbiotic interaction between host and organism" RELATED [] synonym: "symbiotic interaction between organisms" RELATED [] synonym: "symbiotic interaction between species" RELATED [] synonym: "symbiotic process" RELATED [] +xref: Reactome:R-HSA-9839923 "Dengue Virus Infection" is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14807" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] id: GO:0044409 @@ -7458,6 +7391,7 @@ xref: Reactome:R-HSA-173107 "Binding and entry of HIV virion" is_a: GO:0051701 ! biological process involved in interaction with host is_a: GO:0051704 ! multi-organism process property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18563" xsd:anyURI [Term] id: GO:0044419 @@ -7473,6 +7407,7 @@ synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] xref: Reactome:R-HSA-9824443 "Parasitic Infection Pathways" is_a: GO:0008150 ! biological_process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] id: GO:0048609 @@ -7485,6 +7420,7 @@ synonym: "organismal reproductive process" BROAD [] synonym: "reproductive process in a multicellular organism" EXACT [] xref: Reactome:R-HSA-1474165 "Reproduction" is_a: GO:0022414 ! reproductive process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI [Term] id: GO:0051234 @@ -7512,8 +7448,10 @@ synonym: "growth of symbiont in host organelle" NARROW [] synonym: "growth of symbiont in host vacuole" NARROW [] synonym: "interaction with host" EXACT [] xref: Reactome:R-HSA-9635486 "Infection with Mycobacterium tuberculosis" +xref: Reactome:R-HSA-9640148 "Infection with Enterobacteria" xref: Reactome:R-HSA-9658195 "Leishmania infection" is_a: GO:0044403 ! biological process involved in symbiotic interaction +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] id: GO:0051704 @@ -7536,17 +7474,15 @@ property_value: IAO:0000119 "OBI_0000349" xsd:string [Term] id: IAO:0000003 name: measurement unit label -def: "A data item label that denotes a unit of measure." [] -is_a: IAO:0000009 ! data item label +def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." [] +is_a: IAO:0000009 ! datum label property_value: IAO:0000111 "measurement unit label" xsd:string property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string -property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." xsd:string property_value: IAO:0000116 "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: IAO:0000005 @@ -7600,18 +7536,14 @@ is_obsolete: true [Term] id: IAO:0000009 -name: data item label +name: datum label def: "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" [] is_a: IAO:0000030 ! information content entity -property_value: IAO:0000111 "data item label" xsd:string property_value: IAO:0000111 "datum label" xsd:string -property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n" xsd:string property_value: IAO:0000117 "GROUP: IAO" xsd:string -property_value: IAO:0000118 "datum label" xsd:string property_value: IAO:0000232 "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. \n" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: IAO:0000010 @@ -7730,9 +7662,10 @@ property_value: IAO:0000119 "OBI_0000058" xsd:string [Term] id: IAO:0000027 -name: data item -def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] +name: data entity +def: "An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity +property_value: IAO:0000111 "data entity" xsd:string property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -7745,6 +7678,7 @@ property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000118 "data" xsd:string +property_value: IAO:0000118 "data item" xsd:string [Term] id: IAO:0000028 @@ -7799,14 +7733,12 @@ id: IAO:0000032 name: scalar measurement datum def: "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." [] is_a: IAO:0000109 ! measurement datum -property_value: IAO:0000111 "scalar measurement datum" xsd:string property_value: IAO:0000112 "10 feet. 3 ml." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" xsd:string property_value: IAO:0000116 "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: IAO:0000033 @@ -8077,21 +8009,22 @@ property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000119 "OBI_0000187" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/172 [Term] id: IAO:0000100 -name: data set +name: homogenous data collection def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." [] -is_a: IAO:0000027 ! data item -property_value: IAO:0000111 "data set" xsd:string +is_a: IAO:0001000 ! data collection +property_value: IAO:0000111 "homogenous data collection" xsd:string property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string property_value: IAO:0000116 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000118 "data set" xsd:string property_value: IAO:0000119 "group:OBI" xsd:string -property_value: IAO:0000119 "OBI_0000042" xsd:string [Term] id: IAO:0000101 @@ -8110,7 +8043,7 @@ property_value: IAO:0000119 "OBI_0000030" xsd:string id: IAO:0000102 name: data about an ontology part def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000111 "data about an ontology part" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string @@ -8153,7 +8086,7 @@ is_obsolete: true id: IAO:0000109 name: measurement datum def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000111 "measurement datum" xsd:string property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -8161,7 +8094,6 @@ property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:st property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 "group:OBI" xsd:string property_value: IAO:0000119 "OBI_0000305" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: IAO:0000128 @@ -8206,7 +8138,7 @@ property_value: IAO:0000118 "batch number" xsd:string id: IAO:0000140 name: setting datum def: "A settings datum is a datum that denotes some configuration of an instrument." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2/3/2009 Feedback from OBI\n\nThis should be a \"setting specification\". There is a question of whether it is information about a realizable or not.\n\nPro other specification are about realizables.\nCons sometimes specifies a quality which is not a realizable." xsd:string property_value: IAO:0000116 "Alan grouped these in placeholder for the moment. Name by analogy to measurement datum." xsd:string @@ -8483,7 +8415,7 @@ property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "published document" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/232 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/232 [Term] id: IAO:0000312 @@ -8529,7 +8461,7 @@ property_value: IAO:0000112 "The profusion of high-throughput instruments and th property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "precis" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000316 @@ -8544,7 +8476,7 @@ property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "background" xsd:string property_value: IAO:0000118 "introduction" xsd:string property_value: IAO:0000118 "overview" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000317 @@ -8563,7 +8495,7 @@ property_value: IAO:0000118 "experimental section" xsd:string property_value: IAO:0000118 "method" xsd:string property_value: IAO:0000118 "methodology" xsd:string property_value: IAO:0000118 "methods" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000318 @@ -8588,7 +8520,7 @@ property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "discussion" xsd:string property_value: IAO:0000118 "discussion section" xsd:string property_value: IAO:0000118 "discussions" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000320 @@ -8604,7 +8536,7 @@ property_value: IAO:0000118 "literature cited" xsd:string property_value: IAO:0000118 "reference" xsd:string property_value: IAO:0000118 "reference list" xsd:string property_value: IAO:0000118 "references" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000321 @@ -8643,7 +8575,7 @@ property_value: IAO:0000118 "authors' contributions" xsd:string property_value: IAO:0000118 "authors' roles" xsd:string property_value: IAO:0000118 "contributions by the authors" xsd:string property_value: IAO:0000118 "contributorship" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000324 @@ -8658,7 +8590,7 @@ property_value: IAO:0000118 "acknowledgement" xsd:string property_value: IAO:0000118 "acknowledgements" xsd:string property_value: IAO:0000118 "acknowledgment" xsd:string property_value: IAO:0000118 "acknowledgments" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000325 @@ -8672,7 +8604,7 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000118 "endnote" xsd:string property_value: IAO:0000118 "footnotes" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000326 @@ -8697,7 +8629,7 @@ property_value: IAO:0000118 "supplementary information" xsd:string property_value: IAO:0000118 "supplementary material" xsd:string property_value: IAO:0000118 "supplementary materials" xsd:string property_value: IAO:0000118 "supporting information" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000327 @@ -8740,7 +8672,7 @@ property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string id: IAO:0000400 name: cartesian spatial coordinate datum def: "A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude" [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity relationship: IAO:0000219 BFO:0000018 ! denotes zero-dimensional spatial region property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617" xsd:string @@ -8861,9 +8793,8 @@ id: IAO:0000443 name: data item extraction from journal article def: "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000013 ! has_specified_input journal article -relationship: OBI:0000299 IAO:0000027 ! has specified output data item +relationship: OBI:0000293 IAO:0000013 ! has specified input journal article +relationship: OBI:0000299 IAO:0000027 ! has specified output data entity property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string @@ -8871,12 +8802,12 @@ property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string id: IAO:0000444 name: publishing process def: "A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free." [] -is_a: OBI:0000011 ! planned process +is_a: COB:0000035 ! completely executed planned process property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Jie Zheng" xsd:string property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Publishing" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/232 property_value: IAO:0000234 "VEuPathDB" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/232 [Term] id: IAO:0000445 @@ -8886,16 +8817,15 @@ is_a: IAO:0000310 ! document property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "EFO_0001795 in preparation" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/232 property_value: IAO:0000234 "VEuPathDB" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/232 [Term] id: IAO:0000572 name: documenting def: "A planned process in which a document is created or added to by including the specified input in it." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity +relationship: OBI:0000293 IAO:0000030 ! has specified input information content entity relationship: OBI:0000299 IAO:0000310 ! has specified output document property_value: IAO:0000112 "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -8921,7 +8851,6 @@ id: IAO:0000574 name: assigning a centrally registered identifier def: "A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity" [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process relationship: OBI:0000299 IAO:0000577 ! has specified output centrally registered identifier symbol relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry property_value: IAO:0000112 "A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned." xsd:string @@ -8936,8 +8865,8 @@ property_value: IAO:0000118 "assigning a CRID" xsd:string id: IAO:0000575 name: associating information with a centrally registered identifier in its registry def: "A planned process in which a CRID registry associates an information content entity with a CRID symbol" [] -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol +is_a: COB:0000035 ! completely executed planned process +relationship: OBI:0000293 IAO:0000577 ! has specified input centrally registered identifier symbol relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry property_value: IAO:0000112 "Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. " xsd:string property_value: IAO:0000114 IAO:0000120 @@ -9000,15 +8929,14 @@ property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "CRID registry" xsd:string property_value: IAO:0000119 "Original proposal from Bjoern, discussions at IAO calls" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0000580 name: looking up a centrally registered identifier def: "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol" [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000577 ! has_specified_input centrally registered identifier symbol +relationship: OBI:0000293 IAO:0000577 ! has specified input centrally registered identifier symbol relationship: OBI:0000299 IAO:0000030 ! has specified output information content entity relationship: RO:0000057 IAO:0000579 ! has participant centrally registered identifier registry property_value: IAO:0000112 "Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. " xsd:string @@ -9031,7 +8959,7 @@ property_value: IAO:0000114 IAO:0000123 id: IAO:0000584 name: time sampled measurement data set def: "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time." [] -is_a: IAO:0000100 ! data set +is_a: IAO:0000100 ! homogenous data collection relationship: has_part IAO:0000582 ! time stamped measurement datum property_value: IAO:0000112 "pmid:20604925 - time-lapse live cell microscopy" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -9110,7 +9038,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "abbreviation textual entity" xsd:string property_value: IAO:0000112 "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nBAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000606 @@ -9133,8 +9061,8 @@ property_value: IAO:0000118 "list of abbreviations used" xsd:string property_value: IAO:0000118 "non-standard abbreviations" xsd:string property_value: IAO:0000118 "nonstandard abbreviations" xsd:string property_value: IAO:0000118 "nonstandard abbreviations and acronyms" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000607 @@ -9149,8 +9077,8 @@ property_value: IAO:0000118 "author information" xsd:string property_value: IAO:0000118 "authors’ information" xsd:string property_value: IAO:0000118 "biographies" xsd:string property_value: IAO:0000118 "contributor information" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000608 @@ -9160,7 +9088,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "author information textual entity" xsd:string property_value: IAO:0000112 "From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/):\n\nIT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000609 @@ -9175,7 +9103,7 @@ property_value: IAO:0000118 "author summary" xsd:string property_value: IAO:0000118 "summary" xsd:string property_value: IAO:0000118 "synopsis" xsd:string property_value: IAO:0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000610 @@ -9186,7 +9114,7 @@ property_value: IAO:0000111 "author summary textual entity" xsd:string property_value: IAO:0000112 "From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/):\n\n\nThe search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000119 "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000611 @@ -9203,8 +9131,8 @@ property_value: IAO:0000118 "data archiving" xsd:string property_value: IAO:0000118 "data availability" xsd:string property_value: IAO:0000118 "data availability statement" xsd:string property_value: IAO:0000118 "data sharing statement" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000612 @@ -9214,7 +9142,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "availability textual entity" xsd:string property_value: IAO:0000112 "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\nProject home page:http://krux.googlecode.com" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000613 @@ -9227,7 +9155,7 @@ property_value: IAO:0000112 "The section labelled 'case report' in a typical sci property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "case presentation" xsd:string property_value: IAO:0000118 "case report" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000614 @@ -9237,7 +9165,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "case report textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/):\n\nThe patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000615 @@ -9253,7 +9181,7 @@ property_value: IAO:0000118 "conclusion" xsd:string property_value: IAO:0000118 "conclusions" xsd:string property_value: IAO:0000118 "findings" xsd:string property_value: IAO:0000118 "summary" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000616 @@ -9279,8 +9207,8 @@ property_value: IAO:0000118 "disclosure of conflict of interest" xsd:string property_value: IAO:0000118 "disclosure of potential conflicts of interest" xsd:string property_value: IAO:0000118 "duality of interest" xsd:string property_value: IAO:0000118 "statement of interest" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000617 @@ -9290,7 +9218,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "conflict of interest statement" xsd:string property_value: IAO:0000112 "SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] " xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000618 @@ -9302,7 +9230,7 @@ property_value: IAO:0000111 "consent section" xsd:string property_value: IAO:0000112 "The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "consent" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000619 @@ -9312,7 +9240,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "consent textual entity" xsd:string property_value: IAO:0000112 "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nWritten informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000620 @@ -9327,8 +9255,8 @@ property_value: IAO:0000118 "ethical approval" xsd:string property_value: IAO:0000118 "ethical requirements" xsd:string property_value: IAO:0000118 "ethics" xsd:string property_value: IAO:0000118 "ethics statement" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000621 @@ -9339,7 +9267,7 @@ relationship: IAO:0000136 OBI:0500000 ! is about study design property_value: IAO:0000111 "ethical approval textual entity" xsd:string property_value: IAO:0000112 "From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):\n\nThe NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000622 @@ -9351,7 +9279,7 @@ property_value: IAO:0000111 "figures section" xsd:string property_value: IAO:0000112 "The section labelled 'figures' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "figures" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000623 @@ -9373,8 +9301,8 @@ property_value: IAO:0000118 "role of the funding source" xsd:string property_value: IAO:0000118 "source of funding" xsd:string property_value: IAO:0000118 "sources of funding" xsd:string property_value: IAO:0000118 "study funding" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000624 @@ -9384,7 +9312,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "funding souce declaration textual entity" xsd:string property_value: IAO:0000112 "From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/):\n\nThis study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000625 @@ -9408,8 +9336,8 @@ property_value: IAO:0000118 "future research directions" xsd:string property_value: IAO:0000118 "future studies" xsd:string property_value: IAO:0000118 "future work" xsd:string property_value: IAO:0000118 "outlook" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000626 @@ -9419,7 +9347,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "future directions textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/):\n\nIn the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000627 @@ -9431,7 +9359,7 @@ property_value: IAO:0000111 "genome announcement section" xsd:string property_value: IAO:0000112 "The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "genome announcement" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000628 @@ -9441,7 +9369,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "genome announcement textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/):\n\nHere we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000629 @@ -9451,7 +9379,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "keyword textual entity" xsd:string property_value: IAO:0000112 "From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/):\n\nExon orthology; alternative splicing; exon duplication; intron-exon structure." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000630 @@ -9463,7 +9391,7 @@ property_value: IAO:0000111 "keywords section" xsd:string property_value: IAO:0000112 "The section labelled 'keywords' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "keywords" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000631 @@ -9478,7 +9406,7 @@ property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "limitations" xsd:string property_value: IAO:0000118 "study limitations" xsd:string property_value: IAO:0000119 "Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000632 @@ -9489,7 +9417,7 @@ property_value: IAO:0000111 "study limitations textual entity" xsd:string property_value: IAO:0000112 "Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). \n\nOwing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000119 "Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000633 @@ -9500,7 +9428,7 @@ property_value: IAO:0000111 "materials section" xsd:string property_value: IAO:0000112 "The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "materials" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000634 @@ -9511,7 +9439,7 @@ property_value: IAO:0000111 "notes section" xsd:string property_value: IAO:0000112 "The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "notes" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000635 @@ -9522,7 +9450,7 @@ relationship: has_part IAO:0000636 ! patients textual entity property_value: IAO:0000111 "patients section" xsd:string property_value: IAO:0000112 "The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000636 @@ -9532,7 +9460,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "patients textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/):\n\nBetween January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000637 @@ -9545,7 +9473,7 @@ property_value: IAO:0000112 "The section labelled 'pre-publication history' in a property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "notice of republication" xsd:string property_value: IAO:0000118 "pre-publication history" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000638 @@ -9555,7 +9483,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "pre-publication history textual entity" xsd:string property_value: IAO:0000112 "From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/):\n\nThe pre-publication history for this paper can be accessed here:\nhttp://www.biomedcentral.com/1471-2253/13/33/prepub" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000639 @@ -9568,7 +9496,7 @@ property_value: IAO:0000112 "The section labelled 'related work' in a typical sc property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "related literature" xsd:string property_value: IAO:0000118 "related work" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000640 @@ -9578,7 +9506,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "related work textual entity" xsd:string property_value: IAO:0000112 "Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/):\n\nOur work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).\n\n" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000641 @@ -9590,7 +9518,7 @@ property_value: IAO:0000111 "requirements section" xsd:string property_value: IAO:0000112 "The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/)." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "requirements" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000642 @@ -9600,7 +9528,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "requirements textual entity" xsd:string property_value: IAO:0000112 "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\n• Operating systems: Platform independent\n\n• Programming language: Matlab, R, Python\n\n• Other requirements: None\n\n• License: GNU GPL v3\n\n• Any restrictions to use by non-academics: None" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000643 @@ -9610,7 +9538,7 @@ is_a: IAO:0000300 ! textual entity property_value: IAO:0000111 "statistical analysis textual entity" xsd:string property_value: IAO:0000112 "From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/):\n\nData were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000644 @@ -9622,7 +9550,7 @@ property_value: IAO:0000111 "statistical analysis section" xsd:string property_value: IAO:0000112 "The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)" xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "statistical analysis" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000645 @@ -9634,7 +9562,7 @@ property_value: IAO:0000111 "tables section" xsd:string property_value: IAO:0000112 "The section labelled 'tables' in a typical scientific journal article." xsd:string property_value: IAO:0000117 "PERSON: Bill Baumgartner" xsd:string property_value: IAO:0000118 "tables" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/183 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/183 [Term] id: IAO:0000646 @@ -9663,8 +9591,7 @@ id: IAO:0000650 name: database extract, transform, and load process def: "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -relationship: OBI:0000293 IAO:0000030 ! has_specified_input information content entity +relationship: OBI:0000293 IAO:0000030 ! has specified input information content entity relationship: OBI:0000299 IAO:0000030 ! has specified output information content entity property_value: foaf:page https://en.wikipedia.org/wiki/Extract,_transform,_load property_value: IAO:0000111 "database extract, transform, and load process" xsd:string @@ -9673,8 +9600,17 @@ property_value: IAO:0000116 "Alan Ruttenberg 12/21/16: We don't define database property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string property_value: IAO:0000118 "ETL" xsd:string property_value: IAO:0000119 "WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/187 property_value: isDefinedBy https://github.com/information-artifact-ontology/IAO +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/187 + +[Term] +id: IAO:0000651 +name: title section +def: "the section of the document where the title appears" [] +is_a: IAO:0000314 ! document part +property_value: IAO:0000116 "This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself." xsd:string +property_value: IAO:0000117 "Charles Tapley Hoyt" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/286" xsd:anyURI [Term] id: IAO:0000701 @@ -9686,8 +9622,8 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/prisma/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000702 @@ -9701,8 +9637,8 @@ property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/consort/" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/prisma/" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/strobe/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000703 @@ -9716,8 +9652,8 @@ property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/consort/" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/prisma/" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/strobe-nut/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000704 @@ -9729,8 +9665,8 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.equator-network.org/reporting-guidelines/strobe/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000705 @@ -9742,8 +9678,8 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "https://www.ncbi.nlm.nih.gov/books/NBK262175/" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000706 @@ -9755,8 +9691,8 @@ property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chen Yang" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "DOI: 10.1097/PRS.0b013e3181de24bc" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/235 property_value: IAO:0000234 "ONE ontology" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/235 [Term] id: IAO:0000707 @@ -9769,8 +9705,8 @@ property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000117 "PERSON: Tim Beck" xsd:string property_value: IAO:0000118 "visual abstract" xsd:string property_value: IAO:0000119 "https://www.elsevier.com/authors/journal-authors/graphical-abstract" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/234 property_value: IAO:0000234 "Biomedical literature NLP project" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/234 [Term] id: IAO:0000708 @@ -9786,7 +9722,18 @@ property_value: IAO:0000118 "Open Researcher and Contributor Identifier" xsd:str property_value: IAO:0000118 "ORCiD" xsd:string property_value: IAO:0000118 "ORCID ID" xsd:string property_value: IAO:0000119 "https://orcid.org/" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/259" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/259" xsd:string + +[Term] +id: IAO:0001000 +name: data collection +def: "A data entity that consists of multiple data entities." [] +is_a: IAO:0000027 ! data entity +property_value: IAO:0000111 "data collection" xsd:string +property_value: IAO:0000117 "Sebastian Duesing" xsd:string +property_value: IAO:0000118 "data set" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/283" xsd:string +property_value: term_tracker_item "https://github.com/obi-ontology/obi/issues/1877" xsd:string [Term] id: IAO:0020000 @@ -9804,7 +9751,7 @@ property_value: IAO:0000111 "identifier" xsd:string property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "proper name" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020001 @@ -9816,15 +9763,14 @@ property_value: dc:creator "Mathias Brochhausen" xsd:string property_value: IAO:0000112 "alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems" xsd:string property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Grapheme" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020010 name: identifier creating process def: "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." [] is_a: COB:0000035 ! completely executed planned process -is_a: OBI:0000011 ! planned process -intersection_of: OBI:0000011 ! planned process +intersection_of: COB:0000035 ! completely executed planned process intersection_of: OBI:0000299 IAO:0020000 ! has specified output identifier relationship: OBI:0000299 IAO:0020000 ! has specified output identifier property_value: dc:creator "Mathias Brochhausen" xsd:string @@ -9832,7 +9778,7 @@ property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "dubbing process" xsd:string property_value: IAO:0000118 "naming" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020015 @@ -9843,7 +9789,7 @@ is_a: IAO:0020000 ! identifier property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Personal_name" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020016 @@ -9854,7 +9800,7 @@ property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "first name" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Given_name" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020017 @@ -9866,7 +9812,7 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "last name" xsd:string property_value: IAO:0000118 "surname" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Family_name" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0020020 @@ -9888,7 +9834,7 @@ property_value: IAO:0000118 "code system" xsd:string property_value: IAO:0000118 "codeset" xsd:string property_value: IAO:0000118 "coding system" xsd:string property_value: IAO:0000118 "controlled vocabulary" xsd:string -property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +property_value: term_tracker_item "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string [Term] id: IAO:0021003 @@ -15250,7 +15196,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/dideo/dev/dideo.owl" [Term] id: OBI:0000011 name: planned process -def: "A process that realizes a plan which is the concretization of a plan specification." [] +def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string @@ -15275,7 +15221,7 @@ property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string id: OBI:0000066 name: investigation def: "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)." [] -is_a: OBI:0000011 ! planned process +is_a: COB:0000035 ! completely executed planned process property_value: IAO:0000111 "investigation" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl @@ -15336,7 +15282,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: OBI:0000471 name: study design execution def: "a planned process that carries out a study design" [] -is_a: OBI:0000011 ! planned process +is_a: COB:0000035 ! completely executed planned process property_value: IAO:0000111 "study design execution" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl @@ -15374,7 +15320,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: OBI:0000674 name: center value def: "A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "median" xsd:string property_value: IAO:0000111 "center value" xsd:string property_value: IAO:0000114 IAO:0000125 @@ -15387,8 +15333,8 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: OBI:0000679 name: average value def: "A data item that is produced as the output of an averaging data transformation and represents the average value of the input data." [] -is_a: IAO:0000027 ! data item -intersection_of: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity +intersection_of: IAO:0000027 ! data entity intersection_of: OBI:0000312 OBI:0200170 ! is specified output of averaging data transformation relationship: OBI:0000312 OBI:0200170 ! is specified output of averaging data transformation property_value: APOLLO_SV:0000040 "mean" xsd:string @@ -15527,34 +15473,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: OBI:0001847 "study description" xsd:string property_value: OBI:0001886 "project description" xsd:string -[Term] -id: OBI:0001620 -name: latitude coordinate measurement datum -def: "A measurement datum that is the measure of the latitude coordinate of a site." [] -is_a: GEO:000000787 ! geodetic coordinate measurement datum -property_value: dc:source "NIAID GSCID-BRC" xsd:string -property_value: IAO:0000111 "latitude coordinate measurement datum" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string -property_value: IAO:0000118 "latitude" xsd:string -property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: OBI:0001886 "Specimen Collection Location - Latitude" xsd:string - -[Term] -id: OBI:0001621 -name: longitude coordinate measurement datum -def: "A measurement datum that is the measure of the longitude coordinate of a site." [] -is_a: GEO:000000787 ! geodetic coordinate measurement datum -property_value: dc:source "NIAID GSCID-BRC" xsd:string -property_value: IAO:0000111 "longitude coordinate measurement datum" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string -property_value: IAO:0000118 "longitude" xsd:string -property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: OBI:0001886 "Specimen Collection Location - Longitude" xsd:string - [Term] id: OBI:0001628 name: investigation identifier @@ -15582,28 +15500,6 @@ property_value: IAO:0000119 "NIAID GSCID-BRC metadata working group" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: OBI:0001886 "grant ID" xsd:string -[Term] -id: OBI:0001931 -name: scalar value specification -def: "A value specification that consists of two parts: a numeral and a unit label" [] -is_a: OBI:0001933 ! value specification -property_value: IAO:0000111 "scalar value specification" xsd:string -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - -[Term] -id: OBI:0001933 -name: value specification -def: "An information content entity that specifies a value within a classification scheme or on a quantitative scale." [] -is_a: IAO:0000030 ! information content entity -property_value: IAO:0000111 "value specification" xsd:string -property_value: IAO:0000112 "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass." xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000116 "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement." xsd:string -property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - [Term] id: OBI:0001958 name: systematic review study design @@ -15857,7 +15753,9 @@ def: "A process in which at least one bodily component of an organsim participat comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060 is_a: BFO:0000015 ! process relationship: BFO:0000167 OGMS:0000087 ! has participant at all times extended organism +property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://www.jbiomedsem.com/content/1/1/10" xsd:string +property_value: IAO:0000232 "creation date: 2009-06-23T11:53:49Z" xsd:string [Term] id: OGMS:0000063 @@ -16167,10 +16065,11 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] id: OMRSE:00000064 name: school facility -def: "A facility that is run by a school organization and is the bearer of a school function." [] -is_a: OMRSE:00000062 ! facility +def: "An educational facility that is run by a school organization and is the bearer of a school function." [] +is_a: BCIO:026022 ! educational facility relationship: RO:0000053 OMRSE:00000053 ! bearer of school function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-9881-1017 [Term] id: OMRSE:00000065 @@ -16257,13 +16156,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string [Term] id: PATO:0000117 -name: size -namespace: quality -def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [] -subset: attribute_slim -subset: scalar_slim is_a: PATO:0000051 ! morphology -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string [Term] id: PATO:0000122 @@ -16357,18 +16250,6 @@ property_value: IAO:0000111 "physical object quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string -[Term] -id: PATO:0001323 -name: area -namespace: quality -def: "A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent." [] -comment: MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area. -subset: attribute_slim -subset: mpath_slim -subset: scalar_slim -is_a: PATO:0001709 ! 2-D extent -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - [Term] id: PATO:0001708 name: 1-D extent @@ -16376,17 +16257,7 @@ namespace: quality def: "A size quality inhering in an bearer by virtue of the bearer's extension in one dimension." [] subset: attribute_slim synonym: "1-D size" EXACT [] -is_a: PATO:0000117 ! size -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string - -[Term] -id: PATO:0001709 -name: 2-D extent -namespace: quality -def: "A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions." [] -subset: attribute_slim -synonym: "2-D size" EXACT [] -is_a: PATO:0000117 ! size +is_a: PATO:0000117 property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string [Term] @@ -16429,7 +16300,7 @@ name: population def: "A collection of organisms, all of the same species, that live in the same place." [] comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used. is_a: PCO:0000018 ! collection of organisms of the same species -relationship: BFO:0000177 APOLLO_SV:00000104 ! part of continuant at all times biotic ecosystem +relationship: BFO:0000177 APOLLO_SV:00000104 ! biotic ecosystem property_value: APOLLO_SV:0000040 "Population" xsd:string property_value: IAO:0000116 "Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific." xsd:string property_value: IAO:0000119 "ISBN:0878932739" xsd:string @@ -16529,7 +16400,7 @@ property_value: STATO:0000032 "" xsd:string id: STATO:0000258 name: variable def: "A variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation." [] -is_a: IAO:0000027 ! data item +is_a: IAO:0000027 ! data entity property_value: APOLLO_SV:0000040 "variable" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string @@ -16617,8 +16488,6 @@ id: UBERON:0000071 name: death stage def: "End of the life of an organism." [XAO:0000437] subset: common_anatomy -subset: human_subset -subset: mouse_subset synonym: "death" RELATED [] xref: XAO:0000437 xref: XtroDO:0000085 @@ -16630,8 +16499,6 @@ name: life cycle stage def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [https://orcid.org/0000-0002-6601-2165] subset: common_anatomy subset: efo_slim -subset: human_subset -subset: mouse_subset subset: upper_level synonym: "developmental stage" NARROW [] synonym: "stage" NARROW [] @@ -16840,8 +16707,6 @@ id: UBERON:0035943 name: life cycle temporal boundary def: "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity." [https://orcid.org/0000-0002-6601-2165] subset: common_anatomy -subset: human_subset -subset: mouse_subset subset: upper_level is_a: BFO:0000035 ! process boundary @@ -16855,6 +16720,7 @@ property_value: IAO:0000412 "http://purl.org/obo/owl/unit" xsd:string [Term] id: UO:0000001 name: length unit +def: "A unit which is a standard measure of the distance between two points." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "length unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl @@ -16862,6 +16728,7 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000002 name: mass unit +def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "mass unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl @@ -16869,22 +16736,13 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000003 name: time unit +def: "A unit which is a standard measure of the dimension in which events occur in sequence." [] is_a: IAO:0000003 ! measurement unit label property_value: APOLLO_SV:0000040 "unitOfTime" xsd:string property_value: IAO:0000111 "time unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl property_value: IAO:0000412 http://purl.org/obo/owl/UO -[Term] -id: UO:0000047 -name: area unit -namespace: unit.ontology -def: "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [] -subset: unit_group_slim -is_a: IAO:0000003 ! measurement unit label -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/uo.owl" xsd:string -created_by: george gkoutos - [Term] id: UO:0000186 name: dimensionless unit @@ -16980,7 +16838,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/vo.owl" xsd:string [Term] id: oboInOwl:ObsoleteClass name: Obsolete Class -property_value: IAO:0000412 "http://www.geneontology.org/formats/oboInOwl" xsd:string [Term] id: oboInOwl:Subset @@ -17138,27 +16995,6 @@ property_value: IAO:0000111 "is aggregate of" xsd:string property_value: IAO:0000118 "aggregate of" xsd:string property_value: IAO:0000118 "aggregate_of" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string -inverse_of: GEO:000000328 ! is in aggregate - -[Typedef] -id: BFO:0000083 -name: occupies spatial region at some time -property_value: BFO:0000179 "located-at-r_st" xsd:string -property_value: BFO:0000180 "occupiesSpatialRegionAt" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)" xsd:string -property_value: IAO:0000116 "BFO2 Reference: independent continuant" xsd:string -property_value: IAO:0000116 "BFO2 Reference: spatial region" xsd:string -property_value: IAO:0000600 "b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])" xsd:string -property_value: IAO:0000601 "every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])" xsd:string -property_value: IAO:0000601 "if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])" xsd:string -property_value: IAO:0000602 "(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] " xsd:string -property_value: IAO:0000602 "(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] " xsd:string -property_value: IAO:0000602 "(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000004 ! independent continuant -range: BFO:0000006 ! spatial region -inverse_of: BFO:0000123 ! has spatial occupant at some time [Typedef] id: BFO:0000108 @@ -17167,25 +17003,11 @@ name: exists at [Typedef] id: BFO:0000110 name: has continuant part at all times -def: "[copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)" [] -property_value: BFO:0000179 "c-has-part_at" xsd:string -property_value: BFO:0000180 "hasContinuantPartAt" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000602 "(iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl is_transitive: true [Typedef] id: BFO:0000111 name: has proper continuant part at all times -def: "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001" [] -property_value: BFO:0000179 "c-has-ppart_at" xsd:string -property_value: BFO:0000180 "hasProperContinuantPartAt" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl is_transitive: true is_a: BFO:0000110 ! has continuant part at all times @@ -17243,18 +17065,6 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl is_a: BFO:0000117 ! has occurrent part -[Typedef] -id: BFO:0000123 -name: has spatial occupant at some time -property_value: BFO:0000179 "r-location-of_st" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region" xsd:string -property_value: IAO:0000600 "[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000006 ! spatial region -range: BFO:0000004 ! independent continuant - [Typedef] id: BFO:0000132 name: part of occurrent @@ -17291,20 +17101,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl is_a: BFO:0000138 ! proper part of occurrent is_a: BFO:0000139 ! temporal part of -[Typedef] -id: BFO:0000137 -name: proper part of continuant at all times -def: "b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001])" [] -property_value: BFO:0000179 "c-ppart-of_at" xsd:string -property_value: BFO:0000180 "properContinuantPartOfAt" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000602 "(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -is_transitive: true -is_a: BFO:0000177 ! part of continuant at all times -inverse_of: BFO:0000187 ! has continuant part at all times that part exists - [Typedef] id: BFO:0000138 name: proper part of occurrent @@ -17406,39 +17202,6 @@ property_value: IAO:0000602 "(forall (x y z t) (if (and (specificallyDependsOnAt property_value: IAO:0000602 "(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] " xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Typedef] -id: BFO:0000177 -name: part of continuant at all times -def: "[copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)" [] -property_value: BFO:0000179 "c-part-of_at" xsd:string -property_value: BFO:0000180 "continuantPartOfAt" xsd:string -property_value: IAO:0000112 "Mary’s arm continuant_part_of Mary in the time of her life prior to her operation" xsd:string -property_value: IAO:0000112 "the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'" xsd:string -property_value: IAO:0000116 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])" xsd:string -property_value: IAO:0000116 "BFO2 Reference: continuant" xsd:string -property_value: IAO:0000116 "BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000600 "b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])" xsd:string -property_value: IAO:0000601 "continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])" xsd:string -property_value: IAO:0000601 "continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])" xsd:string -property_value: IAO:0000601 "continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])" xsd:string -property_value: IAO:0000601 "continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])" xsd:string -property_value: IAO:0000601 "continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])" xsd:string -property_value: IAO:0000601 "if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])" xsd:string -property_value: IAO:0000602 "(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] " xsd:string -property_value: IAO:0000602 "(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] " xsd:string -property_value: IAO:0000602 "(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] " xsd:string -property_value: IAO:0000602 "(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] " xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -is_reflexive: true -is_transitive: true - [Typedef] id: BFO:0000181 name: has proper temporal part @@ -17462,48 +17225,19 @@ domain: BFO:0000040 ! material entity range: BFO:0000015 ! process [Typedef] -id: BFO:0000187 -name: has continuant part at all times that part exists -def: "forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)" [] -property_value: BFO:0000179 "c-has-part-object_at" xsd:string -property_value: IAO:0000112 "[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation" xsd:string -property_value: IAO:0000112 "[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion." xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant" xsd:string -property_value: IAO:0000116 "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region." xsd:string -property_value: IAO:0000116 "This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/bfo.owl" xsd:string -property_value: IAO:0000600 "[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: GEO:000000328 -name: is in aggregate - -[Typedef] -id: GEO:000000329 -name: is subordinate authority of -def: "A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2." [] -comment: \n'is subordinate authority of'\nDomain: governing organization\nRange: governing organization\nFormal properties: transitive, anti-symmetric, irreflexive\nNatural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2. -domain: GEO:000000400 ! governmental organization -range: GEO:000000400 ! governmental organization - -[Typedef] -id: GEO:000000336 -name: has jurisdiction in -comment: It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c.\n\nin other words, it is perfectly fine to say:\na disjoint b\nc has_jurisdiction_in a\nc has_jurisdiction_in b\n\notherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it "United States territory", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities. -domain: GEO:000000400 ! governmental organization -range: GEO:000000375 ! land mass -is_asymmetric: true +id: IAO:0000011 +name: is directed towards +def: "A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality." [] +comment: In the definition source, the relation is called 'is_about'. To avoid confusion with the existing "is about" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion. +property_value: IAO:0000112 "One of my mental representations is directed towards the Pacific Ocean." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person: William Hogan" xsd:string +property_value: IAO:0000119 "https://ceur-ws.org/Vol-1515/regular10.pdf" xsd:string +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/285 [Typedef] id: IAO:0000039 name: has measurement unit label -def: "A relation between a value specification and its unit of measurement." [] -property_value: IAO:0000111 "has measurement unit label" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string range: IAO:0000003 ! measurement unit label is_functional: true is_a: has_part ! has part @@ -17531,7 +17265,6 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/iao.owl" xsd:string domain: IAO:0000030 ! information content entity [Typedef] @@ -17552,7 +17285,7 @@ name: mentioned by def: "Inverse of the relation 'mentions'" [] property_value: dc:date "2022-01-28T07:20:08Z" xsd:dateTime property_value: IAO:0000117 http://orcid.org/0000-0002-8844-9165 -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/250 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/250 [Typedef] id: IAO:0000219 @@ -17609,7 +17342,7 @@ id: IAO:0000235 name: denoted by def: "inverse of the relation 'denotes'" [] property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" xsd:string -property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/206 +property_value: term_tracker_item https://github.com/information-artifact-ontology/IAO/issues/206 domain: BFO:0000001 ! entity range: IAO:0000030 ! information content entity @@ -17685,10 +17418,9 @@ name: results_in [Typedef] id: OBI:0000293 -name: has_specified_input -def: "The inverse property of is_specified_input_of" [] -property_value: IAO:0000111 "has_specified_input" xsd:string -property_value: IAO:0000111 "has_specified_input" xsd:string +name: has specified input +def: "The inverse property of is specified input of" [] +property_value: IAO:0000111 "has specified input" xsd:string property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string @@ -17697,37 +17429,26 @@ property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -domain: OBI:0000011 ! planned process +domain: COB:0000035 ! completely executed planned process is_a: RO:0000057 ! has participant +inverse_of: OBI:0000295 ! is specified input of [Typedef] id: OBI:0000295 -name: is_specified_input_of -property_value: IAO:0000111 "is_specified_input_of" xsd:string -property_value: IAO:0000112 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -is_a: RO:0000056 ! participates in +name: is specified input of [Typedef] id: OBI:0000299 name: has specified output def: "The inverse property of is specified output of" [] property_value: IAO:0000111 "has specified output" xsd:string -property_value: IAO:0000111 "has_specified_output" xsd:string -property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: COB:0000035 ! completely executed planned process -domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000312 ! is specified output of @@ -17741,15 +17462,11 @@ id: OBI:0000312 name: is specified output of def: "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] property_value: IAO:0000111 "is specified output of" xsd:string -property_value: IAO:0000111 "is_specified_output_of" xsd:string -property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string range: COB:0000035 ! completely executed planned process -range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] @@ -17763,16 +17480,6 @@ property_value: IAO:0000119 "PPPB branch derived" xsd:string property_value: IAO:0000232 "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string -[Typedef] -id: OBI:0001938 -name: has value specification -def: "A relation between an information content entity and a value specification that specifies its value." [] -property_value: IAO:0000111 "has value specification" xsd:string -property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string -property_value: IAO:0000119 "OBI" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string - [Typedef] id: OBIB:0000732 name: owns @@ -17866,7 +17573,6 @@ property_value: IAO:0000112 "this blood clot participates in this blood coagulat property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string property_value: IAO:0000118 "participates_in" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: RO:0000057 ! has participant @@ -17883,7 +17589,6 @@ property_value: IAO:0000112 "this investigation has participant this investigato property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: terms:source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant @@ -18448,6 +18153,7 @@ def: "p is causally upstream of, positive effect q iff p is casually upstream of comment: 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 subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: terms:creator https://orcid.org/0000-0002-6601-2165 is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -18457,6 +18163,7 @@ name: causally upstream of, negative effect def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: terms:creator https://orcid.org/0000-0002-6601-2165 is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect diff --git a/apollo_sv.owl b/apollo_sv.owl index 766bc9e..b374813 100644 --- a/apollo_sv.owl +++ b/apollo_sv.owl @@ -27,7 +27,7 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -43,7 +43,7 @@ C87985BA-6A8A-483A-A6B6-63975101F672 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). - 2026-03-13 + 2026-07-19 @@ -189,120 +189,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - - - - US State Two Digit Identifier - - - - - - - - US State Two Letter Abbreviation - - - - - - - - US State Ens Identifier - - - - - - - - UN Numerical Code - - - - - - - - ISO 3166-1-alpha-3 code - - - - - - - - ISO 3166-1-alpha-2 code - - - - - - - - Proposed Apollo Location Code - - - - - - - - ISO 3166-2 code - - - - - - - - geonameid - integer id of record in geonames database - geonameid - - - - - - - - geonames admin1 code - fipscode (subject to change to iso code), see exceptions below, see file admin1Codes.txt for display names of this code; varchar(20) - admin1 code - - - - - - - - geonames admin2 code - code for the second administrative division, a county in the US, see file admin2Codes.txt; varchar(80) - admin2 code - - - - - - - - geonames admin3 code - code for third level administrative division, varchar(20) - admin3 code - - - - - - - - geonames admin4 code - code for fourth level administrative division, varchar(20) - admin4 code - - - - @@ -315,7 +201,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. editor preferred label editor preferred term editor preferred term - editor preferred term~editor preferred label @@ -462,6 +347,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label alternative term @@ -513,14 +399,28 @@ We also have the outstanding issue of how to aim different definitions to differ + term tracker item term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588 + A URL for a request or discussion of an ontology term. + An IRI or similar locator for a request or discussion of an ontology term. An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + IAO:0000233 + external + term_tracker_item + term_tracker_item + The 'tracker item' can associate a tracker with a specific ontology term. The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item term tracker item + @@ -893,14 +793,224 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + + 2025-06-02 + preferred label for community + + + + + + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initialisms + + + 2023-03-03 + abbreviation + + + + + + + + + A synonym type for describing ambiguous synonyms + + + 2023-03-03 + ambiguous synonym + + + + + + + + + A synonym type for describing dubious synonyms + + + 2023-03-03 + dubious synonym + + + + + + + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + + 2023-03-03 + layperson synonym + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + + 2023-03-03 + UK spelling synonym + + + + + + + + + A synonym type for common misspellings + + + 2023-03-03 + misspelling + + + + + + + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + + 2023-03-03 + misnomer + + + + + + + + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + + 2023-07-25 + previous name + + + + + + + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + + 2023-07-27 + legal name + + + + + + + + + CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label + The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + + + 2023-09-30 + INN + International Nonproprietary Name + + + + + + + + + nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis + A synonym type for describing Latin term synonyms. + + + 2023-10-12 + latin term + + + + + + + + + NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. + A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + + + 2023-11-01 + acronym + + + + + + + + + The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`. + Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf. + + + 2025-09-17 + has ontology hierarchical property + + + + + + + + A serial number such as "12324X"; a stop sign; a written proper name such as "OBI + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + + + 2024-03-25 + has symbol + + + + @@ -1150,30 +1260,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - - - - - - - - - - - - - - - - - - - @@ -1255,14 +1341,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - - - @@ -1381,6 +1459,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + @@ -1466,7 +1556,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + 2024-03-18 database_cross_reference has cross-reference @@ -1475,9 +1567,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - has_definition - + @@ -1626,6 +1716,23 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + - - - - - - located-at-r_st - occupiesSpatialRegionAt - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) - BFO2 Reference: independent continuant - BFO2 Reference: spatial region - b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) - every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002]) - if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001]) - (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] - (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] - (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] - - occupies spatial region at some time - - - - @@ -2028,17 +2109,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - c-has-part_at - hasContinuantPartAt - [copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) - b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'. - [copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times' - http://purl.obolibrary.org/obo/bfo.owl - (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] - has continuant part at all times @@ -2049,12 +2120,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - c-has-ppart_at - hasProperContinuantPartAt - b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001 - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'. - http://purl.obolibrary.org/obo/bfo.owl - has proper continuant part at all times @@ -2134,22 +2199,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - r-location-of_st - [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) - [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant - [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region - [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) - - has spatial occupant at some time - - - - @@ -2197,19 +2246,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - c-ppart-of_at - properContinuantPartOfAt - b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001]) - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'. - http://purl.obolibrary.org/obo/bfo.owl - (iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] - - proper part of continuant at all times - + @@ -2371,39 +2408,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - c-part-of_at - continuantPartOfAt - Mary’s arm continuant_part_of Mary in the time of her life prior to her operation - the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. - [copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) - Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. - BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) - BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. - BFO2 Reference: continuant - BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. - [copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' - http://purl.obolibrary.org/obo/bfo.owl - b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) - continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) - continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) - continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) - continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) - continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) - if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) - (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] - (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] - (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] - (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] - (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] - (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] - (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] - - part of continuant at all times - + @@ -2441,72 +2446,17 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - c-has-part-object_at - [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation - [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. - forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) - This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' - [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. - [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) - [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. - [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant - [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. - http://purl.obolibrary.org/obo/bfo.owl - [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) - - has continuant part at all times that part exists - - - - - + - - is in aggregate - - - - - - - - - - - A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2. - -'is subordinate authority of' -Domain: governing organization -Range: governing organization -Formal properties: transitive, anti-symmetric, irreflexive -Natural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2. - is subordinate authority of - - - - - - - - - - - - It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c. - -in other words, it is perfectly fine to say: -a disjoint b -c has_jurisdiction_in a -c has_jurisdiction_in b - -otherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it "United States territory", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities. - a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories. - if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b. - has jurisdiction in + + One of my mental representations is directed towards the Pacific Ocean. + + A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality. + person: William Hogan + https://ceur-ws.org/Vol-1515/regular10.pdf + + In the definition source, the relation is called 'is_about'. To avoid confusion with the existing "is about" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion. + is directed towards @@ -2517,9 +2467,6 @@ otherwise, we'd end up creating some mereological sum of all the islands, c - has measurement unit label - A relation between a value specification and its unit of measurement. - http://purl.obolibrary.org/obo/obi.owl has measurement unit label @@ -2567,12 +2514,10 @@ Pattern of magnetic domains on scattered pieces of a hard disk platter as mark w - This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. - is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. @@ -2580,7 +2525,6 @@ We will try to build it back up by elaborating the various subproperties that ar Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy - http://purl.obolibrary.org/obo/iao.owl is about @@ -2873,26 +2817,20 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - has_specified_input - has_specified_input + + + has specified input see is_input_of example_of_usage - The inverse property of is_specified_input_of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - http://purl.obolibrary.org/obo/obi.owl - has_specified_input + has specified input @@ -2900,14 +2838,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - is_specified_input_of - some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - - Alan Ruttenberg - PERSON:Bjoern Peters - http://purl.obolibrary.org/obo/obi.owl - is_specified_input_of + is specified input of @@ -2915,29 +2846,18 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - has specified output - has_specified_output - has_specified_output The inverse property of is specified output of - The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot - http://purl.obolibrary.org/obo/obi.owl has specified output - has_specified_output @@ -2956,19 +2876,13 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is specified output of - is_specified_output_of - is_specified_output_of A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - http://purl.obolibrary.org/obo/obi.owl is specified output of - is_specified_output_of @@ -2991,16 +2905,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - has value specification - - A relation between an information content entity and a value specification that specifies its value. - PERSON: James A. Overton - OBI - http://purl.obolibrary.org/obo/obi.owl - has value specification - + @@ -3126,7 +3031,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - @@ -3136,7 +3040,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in - http://purl.obolibrary.org/obo/obi.owl participates in @@ -3145,7 +3048,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - @@ -3165,7 +3067,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://purl.obolibrary.org/obo/obi.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -4212,6 +4113,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. + 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 @@ -4226,6 +4128,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. + causally upstream of, negative effect @@ -5710,9 +5613,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A relation between a scalar measurement data item and a number that quantifies it. - The range should probably not be restricted to "float". It makes sense to set it to "real". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now. - http://purl.obolibrary.org/obo/obi.owl has measurement value @@ -5762,6 +5662,61 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + "Habit" in the Theory of Interpersonal Behavior + "Habits" in the Motivation-Opportunities-Abilities + Published + An <individual human behaviour> that results from a learnt stimulus-behaviour co-occurrence. + A learnt stimulus-behaviour co-occurrence can lead to activation or execution of a habitual behaviour. + +Habitual behaviour can be an MoA or outcome depending on how 'habitual behaviour' is described in an intervention. The Behaviour Change-Intervention Ontology includes the class 'outcome behaviour' (definition: Human behavior that is an intervention outcome.), which would not be an MoA. When an intervention targets a habitual behaviour to achieve an outcome behaviour, the former qualifies as an MoA. + habitual behaviour + + + + + + + + + Published + A facility in which formal education is provided to a student population. + educational facility + + + + + + + + + Also referred to in definitions as human behaviour or just behaviour. + walks for 15 mins/day, never eats meat, attends school daily + Published + A <bodily process> of a human that involves co-ordinated contraction of striated muscles controlled by the brain. + A bodily process of a human that involves co-ordinated contraction of striated muscles controlled by the brain. + human behaviour + HumanBehavior + it is concerned with moving skeletal parts to which it is usually attached.' (https://www.collinsdictionary.com/dictionary/english/striped-muscle) + The class human behaviour [BCIO:042000] has been made obsolete. If you want to refer to the behaviour of an individual, refer to individual human behaviour . If you want to refer to the behaviour of a group, refer to population behaviour. + +Striated muscles referred to in the definition do not ordinarily involve cardiac muscles. + +Behaviours are usually in response to an internal or external stimuli. + +Every behaviour is associated with mental processes, but not every mental process is associated with behaviour. For instance, a verbal communication behaviour will involve mental processes to produce speech. However, mental processes associated with listening can occur without a person performing a behaviour. + +'behaviours' can involve a series of activities (e.g., more granular behaviours). + +'A 'striated muscle' can defined as 'a type of contractile tissue that is marked by transverse striations + individual human behaviour + + + + @@ -5953,7 +5908,7 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire - + @@ -5969,7 +5924,6 @@ Even in the case of a simulated disaster scenario where actual ambulances, fire - @@ -6575,7 +6529,7 @@ can't recall whether we should use process or processual_entity for future - + @@ -6584,7 +6538,6 @@ can't recall whether we should use process or processual_entity for future - @@ -7855,7 +7808,6 @@ The time step value and unit are specified using a scalar value specification. - @@ -15133,13 +15085,14 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + An individual behavior of a human being. Matthew Diller William R. Hogan An individual behavior of a human being. - HumanBehavior - individual human behavior + + obsolete individual human behavior + true @@ -17003,6 +16956,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s + A geographical migration of an organism belonging to the species Homo sapiens. Matthew Diller @@ -17183,7 +17137,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition. Matthew Diller William R. Hogan @@ -17378,6 +17332,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s + @@ -18202,7 +18157,7 @@ has specified input some case definition. - + human daily movement behavior An individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time. William R. Hogan @@ -19158,6 +19113,111 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + + + + + + + + + + + + + + + + + + + + + + + + communicability among human beings + A communicability among human beings (homo sapiens). + William R. Hogan + The ability of a pathogen to transmit from one human host to another human host. + HumanToHumanCommunicability + + human-to-human communicability + + + + + + + + + historical infectious disease scenario date + An infectious disease scenario that represents or reconstructs an outbreak or epidemic that actually occurred, usually constrained by observed data. + William R. Hogan + John Levander + + 2026-04-04T19:36:00Z + historical scenario + + + + + + + + + hypothetical infecctious disease scenario + An infectious disease scenario that represents a possible, assumed, projected, or counterfactual outbreak or epidemic, and does not need to correspond to a specific observed event. + William R. Hogan + John Levander + + 2026-04-04T19:52:04Z + hypothetical scenario + + + + + + + + + An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process. + William R. Hogan + + Lucie Contamin + 2026-07-13T14:13:40Z + + antibody administration control strategy + + + + + + + + + + + + + + + A population treatment census that is about one or more antibody administrations to organisms in a population. + William R. Hogan + + Lucie Contamin + 2026-07-13T13:52:47Z + + antibody administration census + + + + @@ -19197,7 +19257,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si - + @@ -19206,7 +19266,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si - @@ -20208,18 +20267,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects @@ -20864,13 +20911,27 @@ By "similar vaccines" we typically mean same pathogen, but could be si - + + completely executed planned process + completely executed planned process + + + + + planned process + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + + planned process + + + + @@ -20997,12 +21058,25 @@ By "similar vaccines" we typically mean same pathogen, but could be si A drug product that is bearer of a clinical drug role. William Hogan + https://orcid.org/0000-0002-9881-1017 We changed the label to 'clinical drug product' because it was clear that the part of the definition re: bearer of a "clinical drug role" made it such. Other drugs don't have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf "drug product", which also required changing the definition here. clinical drug product + + + + + administration of a drug product to an organism + A treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism. + William R. Hogan + drug administration + + + + @@ -21011,6 +21085,7 @@ By "similar vaccines" we typically mean same pathogen, but could be si William R. Hogan + http://orcid.org/0000-0002-9881-1017 The "intention" part is important because of situations, such as that with phenylephrine, where it was not effective for the labeled use. Even when a drug is proven effective for a particular indication, it might not be therapeutic for every indivdiual to whom it is administered. The psychoactive effect is added for illicit drugs such as crack cocaine. We are including prophylactic and diagnostic effects / usage under the more general heading of 'therapeutic'. @@ -21245,92 +21320,10 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - - - - An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii) - William R. Hogan - In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions. - geopolitical entity - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - obsolete aggregate of governmental organizations - An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on. - William R. Hogan - taken over by GEO_0000000401 - obsolete group of governmental organizations - true - - - - - - - - - A geopolitical entity that is self contained and recognizes no higher political authority than itself. - William R. Hogan - nation - true - - - - - - - - - - - - - - - - - - - - - a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority Amanda Hicks William R. Hogan @@ -21366,180 +21359,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common. - Amanda Hicks - Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. - aggregate of major administrative subdivisions - group of major administrative subdivisions - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common. - Amanda Hicks - Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. - aggregate of dependencies - group of dependencies - - - - - - - - - - - - - - - subcontinental land mass - - - - - - - - - contiguous continental land mass - per the definition of 'contiguous' of "being in actual contact : touching along a boundary or at a point", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island. - -At some point, we need an 'adjacent to' relation if BFO doesn't provide it. - -One question is whether this class encompasses fiat parts of islands. - contiguous land mass - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members. - - William R. Hogan - aggregate of governmental organizations - - - - - - - - - A subcontinental land mass that is part of an island and includes part of the land surface of the island. - William R. Hogan - It cannot be a part of the island, for example, that is below water. - contiguous island land mass - - - - - - - - - - - - - - - - - - - - - - aggregate of contiguous land masses - - - - @@ -21591,106 +21410,6 @@ Thus, we are attempting to define things generally enough that they could be reu - - - - - body of water - - - - - - - - - continent - - - - - - - - - land mass - - - - - - - - - island - - - - - - - - - - - - - - - - - - - - - An object aggregate of geographical entities - aggregate of geographical entities - - - - - - - - - - - - - - - - - - - - - aggregate of geographical features - - - - - - - - - - - - - - - - - - - - - aggregate of islands - - - - @@ -21779,190 +21498,6 @@ Note: this definition was taken over from "geopolitical organization". - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common - Amanda Hicks - William R. Hogan - - http://purl.obolibrary.org/obo/omrse.owl - aggregate of geopolitical organizations - - - - - - - - - An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common. - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies. - obsolete aggregate of dependencies - true - - - - - - - - - An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc. - obsolete aggregate of major administrative subdivisions - true - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common - William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl - examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc. - aggregate of sovereign states - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - geodetic coordinate measurement datum - A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum. - Josh Hanna - William R. Hogan - latitude and longitude are key subtypes - geodetic coordinate measurement datum - - - - @@ -21980,16 +21515,6 @@ Date accessed: 2015-04-13 - - - - - planar angular measurement unit label - plane angle measurement unit label - - - - @@ -22079,6 +21604,7 @@ Date accessed: 2015-04-13 A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. + https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z @@ -22275,6 +21801,7 @@ Date accessed: 2015-04-13 The specific behavior of an organism that is associated with reproduction. + https://github.com/geneontology/go-ontology/issues/23491 jl 2012-09-19T16:01:37Z @@ -22306,6 +21833,7 @@ Date accessed: 2015-04-13 A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). + https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Sexual_reproduction biological_process GO:0019953 @@ -22328,6 +21856,7 @@ Date accessed: 2015-04-13 A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells. + https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Asexual_reproduction biological_process parthenogenesis @@ -22357,6 +21886,7 @@ Date accessed: 2015-04-13 A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. + https://github.com/geneontology/go-ontology/issues/27054 jl 2012-09-19T15:56:06Z GO:0019952 @@ -22391,6 +21921,7 @@ Date accessed: 2015-04-13 Any biological process, occurring at the level of a multicellular organism, pertinent to its function. + https://github.com/geneontology/go-ontology/issues/27189 jl 2012-09-19T16:07:47Z GO:0044707 @@ -22421,10 +21952,13 @@ Date accessed: 2015-04-13 A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts. + https://github.com/geneontology/go-ontology/issues/14807 + https://github.com/geneontology/go-ontology/issues/20191 GO:0043298 GO:0044404 GO:0072519 GO:0085031 + Reactome:R-HSA-9839923 commensalism host-pathogen interaction parasitism @@ -22447,6 +21981,12 @@ Date accessed: 2015-04-13 GOC:cc PMID:31257129 + + + + Reactome:R-HSA-9839923 + Dengue Virus Infection + @@ -22457,6 +21997,7 @@ Date accessed: 2015-04-13 Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction. Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. + https://github.com/geneontology/go-ontology/issues/18563 GO:0030260 GO:0044411 @@ -22550,6 +22091,7 @@ Date accessed: 2015-04-13 Any process evolved to enable an interaction with an organism of a different species. + https://github.com/geneontology/go-ontology/issues/20191 Reactome:R-HSA-9824443 interaction with another species interspecies interaction @@ -22582,6 +22124,7 @@ Date accessed: 2015-04-13 The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. + https://github.com/geneontology/go-ontology/issues/27054 organismal reproductive process Reactome:R-HSA-1474165 reproductive process in a multicellular organism @@ -22625,6 +22168,7 @@ Date accessed: 2015-04-13 An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. + https://github.com/geneontology/go-ontology/issues/20191 GO:0044112 GO:0044116 GO:0044117 @@ -22633,6 +22177,7 @@ Date accessed: 2015-04-13 GO:0044123 GO:0044125 Reactome:R-HSA-9635486 + Reactome:R-HSA-9640148 Reactome:R-HSA-9658195 interaction with host growth of symbiont in host @@ -22655,6 +22200,12 @@ Date accessed: 2015-04-13 Reactome:R-HSA-9635486 Infection with Mycobacterium tuberculosis + + + + Reactome:R-HSA-9640148 + Infection with Enterobacteria + @@ -22696,9 +22247,7 @@ Date accessed: 2015-04-13 measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. - - A data item label that denotes a unit of measure. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and @@ -22708,7 +22257,6 @@ of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot - http://purl.obolibrary.org/obo/obi.owl measurement unit label @@ -22784,19 +22332,13 @@ of this, different, term. - data item label datum label - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - An information content entity that is part of some data item and is used to partially define the denotation of that data item. http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO - datum label 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - http://purl.obolibrary.org/obo/obi.owl - data item label datum label @@ -22985,10 +22527,11 @@ Superclass was 'digital entity' + data entity data item Data items include counts of things, analyte concentrations, and statistical summaries. - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. @@ -23004,6 +22547,8 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data + data item + data entity data item @@ -23102,17 +22647,14 @@ Previous. An information content entity is a non-realizable information entity t 1 - scalar measurement datum 10 feet. 3 ml. A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot - http://purl.obolibrary.org/obo/obi.owl scalar measurement datum @@ -23489,6 +23031,7 @@ XML document; The instructions in a XSD file" PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 + data format specification @@ -23497,8 +23040,8 @@ XML document; The instructions in a XSD file" - - data set + + homogenous data collection Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. @@ -23506,9 +23049,9 @@ XML document; The instructions in a XSD file" 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert - OBI_0000042 + data set group:OBI - data set + homogenous data collection @@ -23615,7 +23158,6 @@ superclass was 'digial entity' person:Chris Stoeckert OBI_0000305 group:OBI - http://purl.obolibrary.org/obo/obi.owl measurement datum @@ -24869,7 +24411,6 @@ GO gene ontology - @@ -24893,7 +24434,7 @@ GO gene ontology - + A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. Person: Jie Zheng @@ -24924,7 +24465,6 @@ GO gene ontology - @@ -24970,7 +24510,6 @@ points together with a line. - @@ -24999,7 +24538,7 @@ points together with a line. - + @@ -25121,7 +24660,6 @@ points together with a line. - @@ -26182,7 +25720,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - @@ -26210,6 +25747,19 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta + + + + + the section of the document where the title appears + This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself. + Charles Tapley Hoyt + https://github.com/information-artifact-ontology/IAO/issues/286 + title section + + + + @@ -26354,6 +25904,21 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta + + + + + data collection + A data entity that consists of multiple data entities. + Sebastian Duesing + data set + https://github.com/information-artifact-ontology/IAO/issues/283 + https://github.com/obi-ontology/obi/issues/1877 + data collection + + + + @@ -26420,7 +25985,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - + @@ -26429,7 +25994,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - @@ -37777,7 +37341,6 @@ No imports planned process Injecting mice with a vaccine in order to test its efficacy - A process that realizes a plan which is the concretization of a plan specification. A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some @@ -37807,7 +37370,7 @@ No imports - + investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). @@ -37915,9 +37478,9 @@ for now. - + study design execution - a planned process that carries out a study design + a planned process that carries out a study design study design execution @@ -38238,42 +37801,6 @@ for now. - - - - - latitude coordinate measurement datum - - A measurement datum that is the measure of the latitude coordinate of a site. - Person: Chris Stoeckert, Jie Zheng - latitude - NIAID GSCID-BRC metadata working group - http://purl.obolibrary.org/obo/obi.owl - Specimen Collection Location - Latitude - NIAID GSCID-BRC - latitude coordinate measurement datum - - - - - - - - - longitude coordinate measurement datum - - A measurement datum that is the measure of the longitude coordinate of a site. - Person: Chris Stoeckert, Jie Zheng - longitude - NIAID GSCID-BRC metadata working group - http://purl.obolibrary.org/obo/obi.owl - Specimen Collection Location - Longitude - NIAID GSCID-BRC - longitude coordinate measurement datum - - - - @@ -38311,31 +37838,13 @@ for now. - - - scalar value specification - - A value specification that consists of two parts: a numeral and a unit label - PERSON:Bjoern Peters - http://purl.obolibrary.org/obo/obi.owl - scalar value specification - + - - - value specification - The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. - - An information content entity that specifies a value within a classification scheme or on a quantitative scale. - This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. - PERSON:Bjoern Peters - http://purl.obolibrary.org/obo/obi.owl - value specification - + @@ -38420,7 +37929,6 @@ https://www.doi.org/ A completely executed planned process that produces output data from input data. A data transformation is a process which produces output data from input data - A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone @@ -38557,6 +38065,7 @@ https://www.doi.org/ A matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. + A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design @@ -38714,7 +38223,9 @@ https://www.doi.org/ A process in which at least one bodily component of an organsim participates. + Albert Goldfain http://www.jbiomedsem.com/content/1/1/10 + creation date: 2009-06-23T11:53:49Z From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060 bodily process @@ -39354,7 +38865,7 @@ Amanda Hicks - + @@ -39374,15 +38885,16 @@ Amanda Hicks - + - A facility that is run by a school organization and is the bearer of a school function. + An educational facility that is run by a school organization and is the bearer of a school function. Mathias Brochhausen + school facility @@ -39586,13 +39098,6 @@ Amanda Hicks - A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0000117 - - - size @@ -39725,23 +39230,6 @@ Amanda Hicks - - - - - A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. - http://purl.obolibrary.org/obo/pato.owl - quality - PATO:0001323 - - - - MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area. - area - - - - @@ -39757,21 +39245,6 @@ Amanda Hicks - - - - - A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. - http://purl.obolibrary.org/obo/pato.owl - 2-D size - quality - PATO:0001709 - - 2-D extent - - - - @@ -40101,8 +39574,6 @@ np.average(range(1,11), weights=range(10,0,-1)) death UBERON:0000071 - - death stage @@ -40136,8 +39607,6 @@ np.average(range(1,11), weights=range(10,0,-1)) UBERON:0000105 - - life cycle stage @@ -40471,8 +39940,6 @@ np.average(range(1,11), weights=range(10,0,-1)) A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity. UBERON:0035943 - - life cycle temporal boundary @@ -40501,6 +39968,7 @@ np.average(range(1,11), weights=range(10,0,-1)) length unit + A unit which is a standard measure of the distance between two points. length unit @@ -40512,6 +39980,7 @@ np.average(range(1,11), weights=range(10,0,-1)) mass unit + A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit @@ -40523,6 +39992,7 @@ np.average(range(1,11), weights=range(10,0,-1)) time unit + A unit which is a standard measure of the dimension in which events occur in sequence. unitOfTime @@ -40531,21 +40001,6 @@ np.average(range(1,11), weights=range(10,0,-1)) - - - - - A unit which is a standard measure of the amount of a 2-dimensional flat surface. - http://purl.obolibrary.org/obo/uo.owl - george gkoutos - unit.ontology - UO:0000047 - - area unit - - - - @@ -40762,17 +40217,6 @@ np.average(range(1,11), weights=range(10,0,-1)) - - - - - Amanda Hicks - e.g., the EU - supranational entity - - - - @@ -40806,13 +40250,8 @@ np.average(range(1,11), weights=range(10,0,-1)) - http://www.geneontology.org/formats/oboInOwl - - - Obsolete Class Obsolete Class - obsolete_class @@ -40863,7 +40302,6 @@ np.average(range(1,11), weights=range(10,0,-1)) - angular degree angular degree ° @@ -40871,32 +40309,6 @@ np.average(range(1,11), weights=range(10,0,-1)) - - - - - radian - A unit of measurement of planar angles where a full circle is 2π. Specifically the angle is the length of the arc subtended by the angle divided by the circumference of the circle. - Josh Hanna - William R. Hogan - Technically in the S.I. system it is a derived unit m•m^-1. - rad - radian - - - - - - - - - square mile - An area unit which is equal to the area enclosed by a square in a flat plane which is one mile on every side. - square mile - - - - @@ -41175,6 +40587,20 @@ np.average(range(1,11), weights=range(10,0,-1)) + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + @@ -41185,12 +40611,13 @@ np.average(range(1,11), weights=range(10,0,-1)) - + - - - "An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST] - square meter + + + 2026-04-04T19:54:38Z + + William R. Hogan @@ -41404,18 +40831,12 @@ This interpretation is *not* the same as an at-all-times relation - - - - + - - - @@ -41531,7 +40952,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -41541,51 +40962,8 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -41617,7 +40995,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -41627,51 +41005,8 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -41703,7 +41038,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -41713,51 +41048,8 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -41789,7 +41081,7 @@ This interpretation is *not* the same as an at-all-times relation - + @@ -41799,51 +41091,8 @@ This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 4966a2b..e7e2687 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -17,8 +17,8 @@ These are the current imports in APOLLO_SV | Import | URL | Type | | ------ | --- | ---- | | ro | http://purl.obolibrary.org/obo/ro.owl | slme | -| geo | http://purl.obolibrary.org/obo/geo/dev/geo.owl | mirror | -| ido | http://purl.obolibrary.org/obo/ido.owl | slme | +| geo | http://purl.obolibrary.org/obo/geo/dev/geo.owl | filter | +| ido | http://purl.obolibrary.org/obo/ido.owl | filter | | mf | http://purl.obolibrary.org/obo/mf.owl | slme | | go | http://purl.obolibrary.org/obo/go.owl | slme | | iao | http://purl.obolibrary.org/obo/iao.owl | mirror | @@ -27,6 +27,7 @@ These are the current imports in APOLLO_SV | ogms | http://purl.obolibrary.org/obo/ogms.owl | filter | | uberon | http://purl.obolibrary.org/obo/uberon.owl | filter | | bcio | http://humanbehaviourchange.org/ontology/bcio.owl | custom | +| obi | http://purl.obolibrary.org/obo/obi.owl | filter | ## Components Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 8d7a1fd..701bc0a 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -16,7 +16,7 @@ # 3. [Update repo to latest ODK](update_repo) # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 6ee100eeff7bea98a4fcb53394f21f836ae9386cecca6a38ef47b0c9c6a71fd0 +CONFIG_HASH= afc55bca35421dc2b7d1273d293169c08e8e8eaa6c54c5adbafd71494b774668 # ---------------------------------------- @@ -193,7 +193,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = ro geo ido mf go iao omrse dron ogms uberon bcio +IMPORTS = ro geo ido mf go iao omrse dron ogms uberon bcio obi IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -449,34 +449,6 @@ $(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl $(IMPORTDIR)/ro_terms.txt $(IMPO repair --merge-axiom-annotations true \ $(ANNOTATE_CONVERT_FILE) -## Module for ontology: geo (mirror) -$(IMPORTDIR)/geo_import.owl: $(MIRRORDIR)/geo.owl | all_robot_plugins - $(ROBOT) annotate --input $< --remove-annotations \ - odk:normalize --base-iri http://purl.obolibrary.org/obo \ - --subset-decls true --synonym-decls true \ - --add-source true \ - repair --merge-axiom-annotations true \ - $(ANNOTATE_CONVERT_FILE) - -## Module for ontology: ido (slme) -$(IMPORTDIR)/ido_import.owl: $(MIRRORDIR)/ido.owl $(IMPORTDIR)/ido_terms.txt $(IMPORTSEED) | all_robot_plugins - $(ROBOT) annotate --input $< --remove-annotations \ - odk:normalize --add-source true \ - extract --term-file $(IMPORTDIR)/ido_terms.txt $(T_IMPORTSEED) \ - --copy-ontology-annotations true --force true \ - --individuals exclude \ - --method BOT \ - remove $(foreach p, $(ANNOTATION_PROPERTIES), --term $(p)) \ - --term rdfs:label \ - --term IAO:0000115 \ - --term OMO:0002000 \ - --term-file $(IMPORTDIR)/ido_terms.txt $(T_IMPORTSEED) \ - --select complement --select annotation-properties \ - odk:normalize --base-iri http://purl.obolibrary.org/obo \ - --subset-decls true --synonym-decls true \ - repair --merge-axiom-annotations true \ - $(ANNOTATE_CONVERT_FILE) - ## Module for ontology: mf (slme) $(IMPORTDIR)/mf_import.owl: $(MIRRORDIR)/mf.owl $(IMPORTDIR)/mf_terms.txt $(IMPORTSEED) | all_robot_plugins $(ROBOT) annotate --input $< --remove-annotations \ @@ -594,7 +566,7 @@ mirror-ro: | $(TMPDIR) .PHONY: mirror-geo .PRECIOUS: $(MIRRORDIR)/geo.owl mirror-geo: | $(TMPDIR) - $(ROBOT) convert -I http://purl.obolibrary.org/obo/geo/dev/geo.owl -o $(TMPDIR)/$@.owl + $(ROBOT) remove -I http://purl.obolibrary.org/obo/geo/dev/geo.owl --base-iri http://purl.obolibrary.org/obo/GEO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ## ONTOLOGY: ido @@ -602,7 +574,7 @@ mirror-geo: | $(TMPDIR) .PRECIOUS: $(MIRRORDIR)/ido.owl mirror-ido: | $(TMPDIR) curl -L $(OBOBASE)/ido.owl --create-dirs -o $(TMPDIR)/ido-download.owl --retry 4 --max-time 200 && \ - $(ROBOT) convert -i $(TMPDIR)/ido-download.owl -o $(TMPDIR)/$@.owl + $(ROBOT) remove -i $(TMPDIR)/ido-download.owl --base-iri http://purl.obolibrary.org/obo/IDO_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl ## ONTOLOGY: mf @@ -668,6 +640,14 @@ mirror-bcio: | $(TMPDIR) $(ROBOT) convert -I http://humanbehaviourchange.org/ontology/bcio.owl -o $(TMPDIR)/$@.owl +## ONTOLOGY: obi +.PHONY: mirror-obi +.PRECIOUS: $(MIRRORDIR)/obi.owl +mirror-obi: | $(TMPDIR) + curl -L $(OBOBASE)/obi.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/obi-download.owl --base-iri http://purl.obolibrary.org/obo/COB_ --base-iri http://purl.obolibrary.org/obo/IAO_ --base-iri http://purl.obolibrary.org/obo/OBI_ --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + + $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi diff --git a/src/ontology/apollo_sv-edit.owl b/src/ontology/apollo_sv-edit.owl index ac365b7..a1f11c8 100644 --- a/src/ontology/apollo_sv-edit.owl +++ b/src/ontology/apollo_sv-edit.owl @@ -32,6 +32,7 @@ Import() Import() Import() Import() +Import() Import() Import() Import() @@ -690,6 +691,8 @@ Declaration(Class(obo:APOLLO_SV_00000652)) Declaration(Class(obo:APOLLO_SV_00000653)) Declaration(Class(obo:APOLLO_SV_00000654)) Declaration(Class(obo:APOLLO_SV_00000655)) +Declaration(Class(obo:APOLLO_SV_00000656)) +Declaration(Class(obo:APOLLO_SV_00000657)) Declaration(Class(obo:APOLLO_SV_00000793)) Declaration(Class(obo:APOLLO_SV_00000794)) Declaration(Class(obo:APOLLO_SV_00000795)) @@ -723,6 +726,7 @@ Declaration(Class(obo:BFO_0000040)) Declaration(Class(obo:BFO_0000144)) Declaration(Class(obo:BFO_0000182)) Declaration(Class(obo:CHEBI_36044)) +Declaration(Class(obo:COB_0000026)) Declaration(Class(obo:DOID_0060478)) Declaration(Class(obo:DOID_12205)) Declaration(Class(obo:DOID_12206)) @@ -1334,8 +1338,6 @@ Declaration(Class(obo:NCBITaxon_9935)) Declaration(Class(obo:NCBITaxon_9940)) Declaration(Class(obo:NCBITaxon_9963)) Declaration(Class(obo:OAE_0000055)) -Declaration(Class(obo:OBI_0000011)) -Declaration(Class(obo:OBI_0000047)) Declaration(Class(obo:OBI_0000066)) Declaration(Class(obo:OBI_0000115)) Declaration(Class(obo:OBI_0000227)) @@ -1347,7 +1349,6 @@ Declaration(Class(obo:OBI_0000658)) Declaration(Class(obo:OBI_0000674)) Declaration(Class(obo:OBI_0000679)) Declaration(Class(obo:OBI_0000714)) -Declaration(Class(obo:OBI_0000968)) Declaration(Class(obo:OBI_0001092)) Declaration(Class(obo:OBI_0001173)) Declaration(Class(obo:OBI_0001226)) @@ -1362,7 +1363,6 @@ Declaration(Class(obo:OBI_0001931)) Declaration(Class(obo:OBI_0001933)) Declaration(Class(obo:OBI_0001958)) Declaration(Class(obo:OBI_0002110)) -Declaration(Class(obo:OBI_0100026)) Declaration(Class(obo:OBI_0200000)) Declaration(Class(obo:OBI_0200166)) Declaration(Class(obo:OBI_0200170)) @@ -1583,6 +1583,7 @@ Declaration(AnnotationProperty(dc:source)) Declaration(AnnotationProperty(dc:type)) Declaration(AnnotationProperty(terms:contributor)) Declaration(AnnotationProperty(terms:created)) +Declaration(AnnotationProperty(terms:creator)) Declaration(AnnotationProperty(terms:description)) Declaration(AnnotationProperty(terms:license)) Declaration(AnnotationProperty(terms:title)) @@ -1745,11 +1746,11 @@ AnnotationAssertion(rdfs:label dc:type "dc:type") AnnotationAssertion(rdfs:label oboInOwl:hasAlternativeId "has_alternative_id") -# Annotation Property: oboInOwl:hasBroadSynonym (has_broad_synonym) +# Annotation Property: oboInOwl:hasBroadSynonym (has broad synonym) AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym") -# Annotation Property: oboInOwl:hasDbXref (has cross-reference) +# Annotation Property: oboInOwl:hasDbXref (database_cross_reference) AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") @@ -1765,7 +1766,7 @@ AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") AnnotationAssertion(rdfs:label oboInOwl:hasOBONamespace "has_obo_namespace") -# Annotation Property: oboInOwl:hasRelatedSynonym (has_related_synonym) +# Annotation Property: oboInOwl:hasRelatedSynonym (has related synonym) AnnotationAssertion(rdfs:label oboInOwl:hasRelatedSynonym "has_related_synonym") @@ -2176,7 +2177,7 @@ AnnotationAssertion(rdfs:label obo:BFO_0000185 "has history"@en) ObjectPropertyDomain(obo:BFO_0000185 obo:BFO_0000040) ObjectPropertyRange(obo:BFO_0000185 obo:BFO_0000015) -# Object Property: obo:OBI_0000308 (obo:OBI_0000308) +# Object Property: obo:OBI_0000308 (obsolete_realizes) AnnotationAssertion(owl:deprecated obo:OBI_0000308 "true"^^xsd:boolean) SubObjectPropertyOf(obo:OBI_0000308 oboInOwl:ObsoleteProperty) @@ -2209,7 +2210,7 @@ AnnotationAssertion(obo:IAO_0000412 obo:OMIABIS_0000048 "http://purl.obolibrary. AnnotationAssertion(rdfs:label obo:OMIABIS_0000048 "is owned by"@en) SubObjectPropertyOf(obo:OMIABIS_0000048 owl:topObjectProperty) -# Object Property: obo:RO_0000053 (bearer of) +# Object Property: obo:RO_0000053 (has characteristic) AnnotationAssertion(obo:IAO_0000118 obo:RO_0000053 "bearer of"@en) AnnotationAssertion(obo:IAO_0000118 obo:RO_0000053 "bearer_of"@en) @@ -2522,7 +2523,7 @@ AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000002 "basicRep AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000002 "MB: Here we run into the well know DL problem that we cannot specify that the infectious agent that is transmitted is of the same type that the infectious agent the population is susceptible to."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000002 "basic reproduction number"@en) SubClassOf(obo:APOLLO_SV_00000002 obo:APOLLO_SV_00000043) -SubClassOf(obo:APOLLO_SV_00000002 ObjectIntersectionOf(obo:APOLLO_SV_00000043 ObjectSomeValuesFrom(obo:IAO_0000136 ObjectIntersectionOf(obo:APOLLO_SV_00000115 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:BFO_0000137 obo:APOLLO_SV_00000234))))))) +SubClassOf(obo:APOLLO_SV_00000002 ObjectIntersectionOf(obo:APOLLO_SV_00000043 ObjectSomeValuesFrom(obo:IAO_0000136 ObjectIntersectionOf(obo:APOLLO_SV_00000115 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:BFO_0000137 obo:APOLLO_SV_00000234))))))) # Class: obo:APOLLO_SV_00000003 (population immunity survey) @@ -2543,7 +2544,7 @@ AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000005 "For example, in a simul Even in the case of a simulated disaster scenario where actual ambulances, fire trucks, and people participate, representations of catastrophic events and injuries, etc. take the place of real ones."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000005 "simulating of process of type X"@en) -SubClassOf(obo:APOLLO_SV_00000005 obo:OBI_0000011) +SubClassOf(obo:APOLLO_SV_00000005 obo:COB_0000082) # Class: obo:APOLLO_SV_00000006 (simulation requester identifier) @@ -2723,7 +2724,7 @@ SubClassOf(obo:APOLLO_SV_00000025 obo:APOLLO_SV_00000227) AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000026 "A planned process involving counting numbers of facilities in a specific region."@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000026 "A planned process involving counting numbers of facilities in a specific region."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000026 "facility survey"@en) -SubClassOf(obo:APOLLO_SV_00000026 obo:OBI_0000011) +SubClassOf(obo:APOLLO_SV_00000026 obo:COB_0000082) # Class: obo:APOLLO_SV_00000027 (school facility census) @@ -2738,8 +2739,8 @@ SubClassOf(obo:APOLLO_SV_00000027 obo:APOLLO_SV_00000173) AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000029 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease."@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000029 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000029 "infectious disease control strategy execution"@en) -EquivalentClasses(obo:APOLLO_SV_00000029 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectSomeValuesFrom(obo:RO_0000059 ObjectIntersectionOf(obo:IAO_0000104 ObjectSomeValuesFrom(obo:BFO_0000051 obo:APOLLO_SV_00000075)))))) -SubClassOf(obo:APOLLO_SV_00000029 obo:OBI_0000011) +EquivalentClasses(obo:APOLLO_SV_00000029 ObjectIntersectionOf(obo:COB_0000082 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectSomeValuesFrom(obo:RO_0000059 ObjectIntersectionOf(obo:IAO_0000104 ObjectSomeValuesFrom(obo:BFO_0000051 obo:APOLLO_SV_00000075)))))) +SubClassOf(obo:APOLLO_SV_00000029 obo:COB_0000082) # Class: obo:APOLLO_SV_00000030 (hospital patient population) @@ -2769,19 +2770,11 @@ AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000032 "count"@en) EquivalentClasses(obo:APOLLO_SV_00000032 ObjectIntersectionOf(obo:IAO_0000027 ObjectSomeValuesFrom(obo:OBI_0000312 obo:APOLLO_SV_00000033))) SubClassOf(obo:APOLLO_SV_00000032 obo:IAO_0000109) -# Class: obo:APOLLO_SV_00000033 (counting) - -AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000033 "The planned process of finding the number of elements in a finite set of objects."@en) -AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000033 "Mathias Brochhausen") -AnnotationAssertion(obo:IAO_0000119 obo:APOLLO_SV_00000033 "http://en.wikipedia.org/wiki/Counting") -AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000033 "The planned process of finding the number of elements in a finite set of objects."@en) -AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000033 "counting"@en) - # Class: obo:APOLLO_SV_00000034 (simulation of organism) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000034 "A simulation that is about an organism") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000034 "simulation of organism"@en) -EquivalentClasses(obo:APOLLO_SV_00000034 ObjectIntersectionOf(ObjectIntersectionOf(obo:APOLLO_SV_00000070 ObjectSomeValuesFrom(obo:APOLLO_SV_00000067 obo:OBI_0100026)) ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000005))) +EquivalentClasses(obo:APOLLO_SV_00000034 ObjectIntersectionOf(ObjectIntersectionOf(obo:APOLLO_SV_00000070 ObjectSomeValuesFrom(obo:APOLLO_SV_00000067 obo:COB_0000022)) ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000005))) # Class: obo:APOLLO_SV_00000036 (normal distribution) @@ -2819,7 +2812,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000041 "A simulated organism AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000041 "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’ However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’ The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000041 "simulation of recovered organism"@en) -EquivalentClasses(obo:APOLLO_SV_00000041 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:APOLLO_SV_00000067 ObjectIntersectionOf(obo:OBI_0100026 ObjectComplementOf(ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172)))) ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000005))) +EquivalentClasses(obo:APOLLO_SV_00000041 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:APOLLO_SV_00000067 ObjectIntersectionOf(obo:COB_0000022 ObjectComplementOf(ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172)))) ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000005))) SubClassOf(obo:APOLLO_SV_00000041 obo:APOLLO_SV_00000034) # Class: obo:APOLLO_SV_00000042 (simulation of disease) @@ -2840,7 +2833,7 @@ AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000043 "The number of suscep AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000043 "ReproductionNumber") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000043 "reproduction number"@en) SubClassOf(obo:APOLLO_SV_00000043 obo:OBI_0000679) -SubClassOf(obo:APOLLO_SV_00000043 ObjectIntersectionOf(obo:OBI_0000679 ObjectSomeValuesFrom(obo:IAO_0000136 ObjectIntersectionOf(obo:APOLLO_SV_00000115 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:BFO_0000137 obo:PCO_0000001))))))) +SubClassOf(obo:APOLLO_SV_00000043 ObjectIntersectionOf(obo:OBI_0000679 ObjectSomeValuesFrom(obo:IAO_0000136 ObjectIntersectionOf(obo:APOLLO_SV_00000115 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:BFO_0000137 obo:PCO_0000001))))))) # Class: obo:APOLLO_SV_00000044 (nursery school student population) @@ -3004,7 +2997,7 @@ SubClassOf(obo:APOLLO_SV_00000062 obo:APOLLO_SV_00000178) AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000063 "A simulation of an organism in a simulated population that has participated in an epidemic control measure."@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000063 "A simulated organism in a simulated population has participated in a particular simulated control measure. (e.g. an organism received antiviral treatment)"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000063 "simulation of control measure participant"@en) -EquivalentClasses(obo:APOLLO_SV_00000063 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:APOLLO_SV_00000067 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000029))) ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000005))) +EquivalentClasses(obo:APOLLO_SV_00000063 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:APOLLO_SV_00000067 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000029))) ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000005))) SubClassOf(obo:APOLLO_SV_00000063 obo:APOLLO_SV_00000034) # Class: obo:APOLLO_SV_00000064 (simulation time series) @@ -3083,7 +3076,7 @@ SubClassOf(obo:APOLLO_SV_00000071 oboInOwl:ObsoleteClass) AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000072 "A simulation of a susceptible organism in a simulated population."@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000072 "A simulated organism in a simulated population that is capable of acquiring a particular simulated disease."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000072 "simulation of susceptible organism"@en) -EquivalentClasses(obo:APOLLO_SV_00000072 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:APOLLO_SV_00000067 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000005))) +EquivalentClasses(obo:APOLLO_SV_00000072 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:APOLLO_SV_00000067 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000005))) SubClassOf(obo:APOLLO_SV_00000072 obo:APOLLO_SV_00000034) # Class: obo:APOLLO_SV_00000073 (simulation of symptomatic organism) @@ -3218,7 +3211,7 @@ AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000089 "1. Apollo-SV does not d 2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000089 "measured vaccination efficacy"@en) SubClassOf(obo:APOLLO_SV_00000089 obo:IAO_0000109) -SubClassOf(obo:APOLLO_SV_00000089 ObjectIntersectionOf(obo:IAO_0000109 ObjectSomeValuesFrom(obo:IAO_0000136 obo:APOLLO_SV_00000025) ObjectSomeValuesFrom(obo:IAO_0000136 ObjectIntersectionOf(obo:PCO_0000000 ObjectAllValuesFrom(obo:RO_0002351 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000142))))))) +SubClassOf(obo:APOLLO_SV_00000089 ObjectIntersectionOf(obo:IAO_0000109 ObjectSomeValuesFrom(obo:IAO_0000136 obo:APOLLO_SV_00000025) ObjectSomeValuesFrom(obo:IAO_0000136 ObjectIntersectionOf(obo:PCO_0000000 ObjectAllValuesFrom(obo:RO_0002351 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000142))))))) # Class: obo:APOLLO_SV_00000090 (vaccination efficacy study design execution) @@ -3415,7 +3408,7 @@ AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000114 "A process of reprodu AnnotationAssertion(dc:creator obo:APOLLO_SV_00000114 "M. Brochhausen"@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000114 "infection is reproduction of a pathogen inside some tissue of a host. By associating infection with the classes latent period and infectious period, which are associated with specific pathogen species and host species, Apollo-SV defines infection further as reproduction of a particular pathogen taxon inside some tissue of a particular host taxon."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000114 "infection"@en) -EquivalentClasses(obo:APOLLO_SV_00000114 ObjectIntersectionOf(obo:APOLLO_SV_00000651 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(obo:UBERON_0000479 ObjectSomeValuesFrom(obo:BFO_0000050 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000114 ObjectIntersectionOf(obo:APOLLO_SV_00000651 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(obo:UBERON_0000479 ObjectSomeValuesFrom(obo:BFO_0000050 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000114 obo:APOLLO_SV_00000651) SubClassOf(obo:APOLLO_SV_00000114 ObjectSomeValuesFrom(obo:RO_0002087 obo:APOLLO_SV_00000115)) @@ -3432,7 +3425,7 @@ The likelihood of acquisition is expressed by parameters such as the basic repro An infection is acquired from an infectious organism or a contaminated thing."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000115 "Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000115 "infection acquisition"@en) -EquivalentClasses(obo:APOLLO_SV_00000115 ObjectIntersectionOf(obo:GO_0044409 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectUnionOf(obo:APOLLO_SV_00000166 ObjectIntersectionOf(obo:APOLLO_SV_00000238 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000182)))) ObjectSomeValuesFrom(obo:RO_0002411 obo:APOLLO_SV_00000114))) +EquivalentClasses(obo:APOLLO_SV_00000115 ObjectIntersectionOf(obo:GO_0044409 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectUnionOf(obo:APOLLO_SV_00000166 ObjectIntersectionOf(obo:APOLLO_SV_00000238 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000182)))) ObjectSomeValuesFrom(obo:RO_0002411 obo:APOLLO_SV_00000114))) SubClassOf(obo:APOLLO_SV_00000115 obo:GO_0044409) # Class: obo:APOLLO_SV_00000117 (vaccine identifier) @@ -3633,7 +3626,7 @@ AnnotationAssertion(obo:IAO_0000119 obo:APOLLO_SV_00000142 "http://en.wikipedia. AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000142 "A treatment of an individual with antigenic material from a pathogen that has the goal of inducing resistance of the individual to infection with the pathogen."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000142 "Vaccination") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000142 "vaccination"@en) -EquivalentClasses(obo:APOLLO_SV_00000142 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000055 ObjectSomeValuesFrom(obo:RO_0000059 ObjectIntersectionOf(obo:IAO_0000104 ObjectSomeValuesFrom(obo:BFO_0000051 obo:APOLLO_SV_00000141)))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:BFO_0000040 ObjectSomeValuesFrom(obo:RO_0000053 obo:VO_0000278))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))))) +EquivalentClasses(obo:APOLLO_SV_00000142 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000055 ObjectSomeValuesFrom(obo:RO_0000059 ObjectIntersectionOf(obo:IAO_0000104 ObjectSomeValuesFrom(obo:BFO_0000051 obo:APOLLO_SV_00000141)))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:BFO_0000040 ObjectSomeValuesFrom(obo:RO_0000053 obo:VO_0000278))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))))) SubClassOf(obo:APOLLO_SV_00000142 obo:OGMS_0000090) # Class: obo:APOLLO_SV_00000143 (obsolete vaccine disposition) @@ -3712,8 +3705,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000152 "A planned process in AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000152 "Mathias Brochhausen"@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000152 "A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000152 "population survey"@en) -EquivalentClasses(obo:APOLLO_SV_00000152 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf(obo:APOLLO_SV_00000033 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectIntersectionOf(obo:APOLLO_SV_00000032 ObjectSomeValuesFrom(obo:IAO_0000136 obo:PCO_0000001))))))) -SubClassOf(obo:APOLLO_SV_00000152 obo:OBI_0000011) +EquivalentClasses(obo:APOLLO_SV_00000152 ObjectIntersectionOf(obo:COB_0000082 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf(obo:APOLLO_SV_00000033 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectIntersectionOf(obo:APOLLO_SV_00000032 ObjectSomeValuesFrom(obo:IAO_0000136 obo:PCO_0000001))))))) +SubClassOf(obo:APOLLO_SV_00000152 obo:COB_0000082) # Class: obo:APOLLO_SV_00000153 (population census) @@ -3895,7 +3888,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000172 "The ability to parti AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000172 "Mathias Brochhausen"@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000172 "The ability to participate in infection acquisition as a host."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000172 "susceptibility"@en) -EquivalentClasses(obo:APOLLO_SV_00000172 ObjectIntersectionOf(obo:BFO_0000016 ObjectAllValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000115) ObjectAllValuesFrom(obo:RO_0000052 ObjectIntersectionOf(obo:OBI_0100026 ObjectComplementOf(obo:APOLLO_SV_00000238))))) +EquivalentClasses(obo:APOLLO_SV_00000172 ObjectIntersectionOf(obo:BFO_0000016 ObjectAllValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000115) ObjectAllValuesFrom(obo:RO_0000052 ObjectIntersectionOf(obo:COB_0000022 ObjectComplementOf(obo:APOLLO_SV_00000238))))) SubClassOf(obo:APOLLO_SV_00000172 obo:BFO_0000016) # Class: obo:APOLLO_SV_00000173 (census) @@ -4013,7 +4006,7 @@ AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000186 "The process of exist AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000186 "Contamination") AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000186 "The preferred term is biological contamination to distinguish from things like radiological contamination, contamination of the Gulf of Mexico with oil, the contamination of air with pollution, etc."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000186 "contamination"@en) -EquivalentClasses(obo:APOLLO_SV_00000186 ObjectUnionOf(ObjectIntersectionOf(obo:APOLLO_SV_00000651 ObjectSomeValuesFrom(obo:RO_0000057 obo:APOLLO_SV_00000237) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:BFO_0000040 ObjectComplementOf(obo:OBI_0100026)))) ObjectIntersectionOf(obo:GO_0008150 ObjectSomeValuesFrom(obo:RO_0000057 obo:APOLLO_SV_00000237) ObjectSomeValuesFrom(obo:RO_0000057 obo:BFO_0000040)))) +EquivalentClasses(obo:APOLLO_SV_00000186 ObjectUnionOf(ObjectIntersectionOf(obo:APOLLO_SV_00000651 ObjectSomeValuesFrom(obo:RO_0000057 obo:APOLLO_SV_00000237) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:BFO_0000040 ObjectComplementOf(obo:COB_0000022)))) ObjectIntersectionOf(obo:GO_0008150 ObjectSomeValuesFrom(obo:RO_0000057 obo:APOLLO_SV_00000237) ObjectSomeValuesFrom(obo:RO_0000057 obo:BFO_0000040)))) SubClassOf(obo:APOLLO_SV_00000186 obo:GO_0008150) # Class: obo:APOLLO_SV_00000187 (population treatment census) @@ -4164,8 +4157,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000205 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000205 "An organism of a particular species that can undergo infection with a particular pathogen."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000205 "susceptible") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000205 "susceptible organism"@en) -EquivalentClasses(obo:APOLLO_SV_00000205 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) -SubClassOf(obo:APOLLO_SV_00000205 obo:OBI_0100026) +EquivalentClasses(obo:APOLLO_SV_00000205 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) +SubClassOf(obo:APOLLO_SV_00000205 obo:COB_0000022) # Class: obo:APOLLO_SV_00000206 (immune organism) @@ -4174,8 +4167,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000206 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000206 "An organism of a particular species that has developed immune resistance to infection with a pathogen of a particular species."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000206 "immune") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000206 "immune organism"@en) -EquivalentClasses(obo:APOLLO_SV_00000206 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000151))) -SubClassOf(obo:APOLLO_SV_00000206 obo:OBI_0100026) +EquivalentClasses(obo:APOLLO_SV_00000206 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000151))) +SubClassOf(obo:APOLLO_SV_00000206 obo:COB_0000022) # Class: obo:APOLLO_SV_00000207 (resistant organism) @@ -4184,8 +4177,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000207 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000207 "An organism of a particular species that is unable to undergo infection with a particular pathogen."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000207 "resistant") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000207 "resistant organism"@en) -EquivalentClasses(obo:APOLLO_SV_00000207 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000145))) -SubClassOf(obo:APOLLO_SV_00000207 obo:OBI_0100026) +EquivalentClasses(obo:APOLLO_SV_00000207 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000145))) +SubClassOf(obo:APOLLO_SV_00000207 obo:COB_0000022) # Class: obo:APOLLO_SV_00000208 (control strategy start time information) @@ -4303,7 +4296,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000220 "Mathias Brochhausen" AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000220 "A material entity that is part of an abiotic ecosystem."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000220 "Class was originally created to correspond with an element from Apollo XSD v3.1.0."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000220 "abiotic ecosystem element"@en) -EquivalentClasses(obo:APOLLO_SV_00000220 ObjectIntersectionOf(ObjectIntersectionOf(obo:BFO_0000040 ObjectComplementOf(obo:OBI_0100026)) ObjectSomeValuesFrom(obo:BFO_0000050 obo:APOLLO_SV_00000100))) +EquivalentClasses(obo:APOLLO_SV_00000220 ObjectIntersectionOf(ObjectIntersectionOf(obo:BFO_0000040 ObjectComplementOf(obo:COB_0000022)) ObjectSomeValuesFrom(obo:BFO_0000050 obo:APOLLO_SV_00000100))) SubClassOf(obo:APOLLO_SV_00000220 obo:BFO_0000040) # Class: obo:APOLLO_SV_00000221 (immune population acting like immune) @@ -4426,7 +4419,7 @@ SubClassOf(obo:APOLLO_SV_00000232 obo:APOLLO_SV_00000509) AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000233 "A population of only infected members of one species."@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000233 "A population of only infected members of one species."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000233 "infected population"@en) -EquivalentClasses(obo:APOLLO_SV_00000233 ObjectIntersectionOf(obo:APOLLO_SV_00000516 ObjectAllValuesFrom(obo:RO_0002351 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:BFO_0000067 obo:APOLLO_SV_00000114))))) +EquivalentClasses(obo:APOLLO_SV_00000233 ObjectIntersectionOf(obo:APOLLO_SV_00000516 ObjectAllValuesFrom(obo:RO_0002351 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:BFO_0000067 obo:APOLLO_SV_00000114))))) SubClassOf(obo:APOLLO_SV_00000233 obo:APOLLO_SV_00000516) # Class: obo:APOLLO_SV_00000234 (susceptible population) @@ -4434,7 +4427,7 @@ SubClassOf(obo:APOLLO_SV_00000233 obo:APOLLO_SV_00000516) AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000234 "A population of organisms that are all susceptible."@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000234 "A population of organisms that are all susceptible."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000234 "susceptible population"@en) -EquivalentClasses(obo:APOLLO_SV_00000234 ObjectIntersectionOf(obo:APOLLO_SV_00000516 ObjectAllValuesFrom(obo:RO_0002351 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))))) +EquivalentClasses(obo:APOLLO_SV_00000234 ObjectIntersectionOf(obo:APOLLO_SV_00000516 ObjectAllValuesFrom(obo:RO_0002351 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))))) SubClassOf(obo:APOLLO_SV_00000234 obo:APOLLO_SV_00000516) # Class: obo:APOLLO_SV_00000235 (immune population) @@ -4455,8 +4448,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000237 "An organism of a par AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000237 "An organism, virus, or prion that can infect another organism."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000237 "pathogen") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000237 "pathogen"@en) -EquivalentClasses(obo:APOLLO_SV_00000237 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000404))) -SubClassOf(obo:APOLLO_SV_00000237 obo:OBI_0100026) +EquivalentClasses(obo:APOLLO_SV_00000237 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000404))) +SubClassOf(obo:APOLLO_SV_00000237 obo:COB_0000022) # Class: obo:APOLLO_SV_00000238 (host organism) @@ -4464,8 +4457,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000238 "An organism of a par AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000238 "An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000238 "host"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000238 "host organism"@en) -EquivalentClasses(obo:APOLLO_SV_00000238 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:BFO_0000067 obo:APOLLO_SV_00000651))) -SubClassOf(obo:APOLLO_SV_00000238 obo:OBI_0100026) +EquivalentClasses(obo:APOLLO_SV_00000238 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:BFO_0000067 obo:APOLLO_SV_00000651))) +SubClassOf(obo:APOLLO_SV_00000238 obo:COB_0000022) # Class: obo:APOLLO_SV_00000239 (infectious disease) @@ -4696,7 +4689,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000264 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000264 "An infection acquisition from a contaminated thing."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000264 "InfectionAcquisitionFromContaminatedAbioticThing") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000264 "infection acquisition from contaminated thing"@en) -EquivalentClasses(obo:APOLLO_SV_00000264 ObjectIntersectionOf(obo:GO_0044409 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) ObjectSomeValuesFrom(obo:RO_0000057 obo:APOLLO_SV_00000166) ObjectSomeValuesFrom(obo:RO_0002411 obo:APOLLO_SV_00000114))) +EquivalentClasses(obo:APOLLO_SV_00000264 ObjectIntersectionOf(obo:GO_0044409 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) ObjectSomeValuesFrom(obo:RO_0000057 obo:APOLLO_SV_00000166) ObjectSomeValuesFrom(obo:RO_0002411 obo:APOLLO_SV_00000114))) SubClassOf(obo:APOLLO_SV_00000264 obo:GO_0044409) # Class: obo:APOLLO_SV_00000265 (infection acquisition from infectious host) @@ -4708,7 +4701,7 @@ AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000265 "An infection acquisi The individual acquiring the infection can be of a different species than the one who is infectious."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000265 "InfectionAcquisitionFromInfectedHost") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000265 "infection acquisition from infectious host"@en) -EquivalentClasses(obo:APOLLO_SV_00000265 ObjectIntersectionOf(obo:GO_0044409 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:APOLLO_SV_00000238 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000182))) ObjectSomeValuesFrom(obo:RO_0002411 obo:APOLLO_SV_00000114))) +EquivalentClasses(obo:APOLLO_SV_00000265 ObjectIntersectionOf(obo:GO_0044409 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000172))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:APOLLO_SV_00000238 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000182))) ObjectSomeValuesFrom(obo:RO_0002411 obo:APOLLO_SV_00000114))) SubClassOf(obo:APOLLO_SV_00000265 obo:GO_0044409) # Class: obo:APOLLO_SV_00000266 (disease surveillance capability) @@ -5033,8 +5026,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000302 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000302 "An organism that has recovered from infection with a particular pathogen, is no longer infectious to other organisms of any species, and is not able to be infected again with that pathogen."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000302 "recovered"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000302 "recovered organism"@en) -EquivalentClasses(obo:APOLLO_SV_00000302 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000301))) -SubClassOf(obo:APOLLO_SV_00000302 obo:OBI_0100026) +EquivalentClasses(obo:APOLLO_SV_00000302 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000301))) +SubClassOf(obo:APOLLO_SV_00000302 obo:COB_0000022) # Class: obo:APOLLO_SV_00000303 (compartmental disease transmission model) @@ -5233,7 +5226,7 @@ AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000330 "A reproduction of a AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000330 "Colonization") AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000330 "Primary use case is colonization of humans, animals with Staph aureus, but it also covers bacteriuria, transient bactermia, and normal gut flora."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000330 "colonization"@en) -EquivalentClasses(obo:APOLLO_SV_00000330 ObjectIntersectionOf(obo:APOLLO_SV_00000651 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(ObjectComplementOf(obo:UBERON_0000479) ObjectSomeValuesFrom(obo:BFO_0000050 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000330 ObjectIntersectionOf(obo:APOLLO_SV_00000651 ObjectSomeValuesFrom(obo:BFO_0000066 ObjectIntersectionOf(ObjectComplementOf(obo:UBERON_0000479) ObjectSomeValuesFrom(obo:BFO_0000050 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000330 obo:APOLLO_SV_00000651) # Class: obo:APOLLO_SV_00000331 (infection in population) @@ -5312,7 +5305,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000337 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000337 "A symbiosis where the organisms that are interacting remain physically external to one another."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000337 "It includes situations where one organism lives on the surface of the other organism."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000337 "ectosymbiosis"@en) -EquivalentClasses(obo:APOLLO_SV_00000337 ObjectIntersectionOf(obo:APOLLO_SV_00000596 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0002163 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000337 ObjectIntersectionOf(obo:APOLLO_SV_00000596 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0002163 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000337 obo:APOLLO_SV_00000596) # Class: obo:APOLLO_SV_00000338 (antagonism) @@ -5333,7 +5326,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000339 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000339 "An ectosymbiosis that results in harm to one of the participating organisms but neither harms nor benefits the other participating organisms."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000339 "Example: Spanish ibex and weevils of the genus Timarcha"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000339 "amensalism"@en) -EquivalentClasses(obo:APOLLO_SV_00000339 ObjectIntersectionOf(obo:APOLLO_SV_00000337 ObjectComplementOf(ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:OGMS_0000032 ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026)))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000371))))) +EquivalentClasses(obo:APOLLO_SV_00000339 ObjectIntersectionOf(obo:APOLLO_SV_00000337 ObjectComplementOf(ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:OGMS_0000032 ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022)))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000371))))) SubClassOf(obo:APOLLO_SV_00000339 obo:APOLLO_SV_00000337) # Class: obo:APOLLO_SV_00000340 (agonism) @@ -5343,7 +5336,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000340 "Matthew Diller") AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000340 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000340 "An ectosymbiosis that results in harm to one of the participating organisms and benefit to another participating organism."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000340 "agonism"@en) -EquivalentClasses(obo:APOLLO_SV_00000340 ObjectIntersectionOf(obo:APOLLO_SV_00000337 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000371))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000372))))) +EquivalentClasses(obo:APOLLO_SV_00000340 ObjectIntersectionOf(obo:APOLLO_SV_00000337 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000371))) ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000372))))) SubClassOf(obo:APOLLO_SV_00000340 obo:APOLLO_SV_00000337) # Class: obo:APOLLO_SV_00000341 (intimate agonism) @@ -5376,7 +5369,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000343 "facultative ectopara AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000343 "An ectosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000343 "Example: Armillaria (type of wood fungus) and trees"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000343 "facultative ectosymbiotic parasitism"@en) -EquivalentClasses(obo:APOLLO_SV_00000343 ObjectIntersectionOf(obo:APOLLO_SV_00000342 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000343 ObjectIntersectionOf(obo:APOLLO_SV_00000342 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000343 obo:APOLLO_SV_00000342) # Class: obo:APOLLO_SV_00000344 (obligatory ectosymbiotic parasitism) @@ -5432,7 +5425,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000348 "William R. Hogan") AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000348 "ectocommensalism"@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000348 "An ectosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000348 "ectosymbiotic commensalism"@en) -EquivalentClasses(obo:APOLLO_SV_00000348 ObjectIntersectionOf(obo:APOLLO_SV_00000337 ObjectComplementOf(ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:OGMS_0000032 ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026)))) ObjectSomeValuesFrom(obo:BFO_0000051 obo:APOLLO_SV_00000372))) +EquivalentClasses(obo:APOLLO_SV_00000348 ObjectIntersectionOf(obo:APOLLO_SV_00000337 ObjectComplementOf(ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:OGMS_0000032 ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022)))) ObjectSomeValuesFrom(obo:BFO_0000051 obo:APOLLO_SV_00000372))) SubClassOf(obo:APOLLO_SV_00000348 obo:APOLLO_SV_00000337) # Class: obo:APOLLO_SV_00000349 (facultative ectosymbiotic commensalism) @@ -5444,7 +5437,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000349 "facultative ectocomm AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000349 "An ectosymbiotic commensalism that realizes a dispostion of the organism that benefits that is not one of its biological functions."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000349 "Example: Ophiodromus pugettensis and Patiria miniata"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000349 "facultative ectosymbiotic commensalism"@en) -EquivalentClasses(obo:APOLLO_SV_00000349 ObjectIntersectionOf(obo:APOLLO_SV_00000348 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000349 ObjectIntersectionOf(obo:APOLLO_SV_00000348 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000349 obo:APOLLO_SV_00000348) # Class: obo:APOLLO_SV_00000350 (obligatory ectosymbiotic commensalism) @@ -5456,7 +5449,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000350 "obligatory ectocomme AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000350 "An ectosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000350 "Example: Basicladia algae and sea turtles"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000350 "obligatory ectosymbiotic commensalism"@en) -EquivalentClasses(obo:APOLLO_SV_00000350 ObjectIntersectionOf(obo:APOLLO_SV_00000348 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:BFO_0000034 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000137 obo:OBI_0100026) ObjectSomeValuesFrom(obo:RO_0000052 obo:UBERON_0000061)))))) +EquivalentClasses(obo:APOLLO_SV_00000350 ObjectIntersectionOf(obo:APOLLO_SV_00000348 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:BFO_0000034 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000137 obo:COB_0000022) ObjectSomeValuesFrom(obo:RO_0000052 obo:UBERON_0000061)))))) SubClassOf(obo:APOLLO_SV_00000350 obo:APOLLO_SV_00000348) # Class: obo:APOLLO_SV_00000351 (ectosymbiotic mutualism) @@ -5479,7 +5472,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000352 "facultative ectomutu AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000352 "An ectosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000352 "Example: ants that feed off of honeydew from aphids, and in turn protect the aphids"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000352 "facultative ectosymbiotic mutualism"@en) -EquivalentClasses(obo:APOLLO_SV_00000352 ObjectIntersectionOf(obo:APOLLO_SV_00000351 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000352 ObjectIntersectionOf(obo:APOLLO_SV_00000351 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000352 obo:APOLLO_SV_00000351) # Class: obo:APOLLO_SV_00000353 (obligatory ectosymbiotic mutualism) @@ -5491,7 +5484,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000353 "obligatory ectomutua AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000353 "An ectosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000353 "Example: bees and flowers"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000353 "obligatory ectosymbiotic mutualism"@en) -EquivalentClasses(obo:APOLLO_SV_00000353 ObjectIntersectionOf(obo:APOLLO_SV_00000351 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:BFO_0000034 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000137 obo:OBI_0100026) ObjectSomeValuesFrom(obo:RO_0000052 obo:UBERON_0000061)))))) +EquivalentClasses(obo:APOLLO_SV_00000353 ObjectIntersectionOf(obo:APOLLO_SV_00000351 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:BFO_0000034 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000137 obo:COB_0000022) ObjectSomeValuesFrom(obo:RO_0000052 obo:UBERON_0000061)))))) SubClassOf(obo:APOLLO_SV_00000353 obo:APOLLO_SV_00000351) # Class: obo:APOLLO_SV_00000354 (endosymbiosis) @@ -5501,7 +5494,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000354 "Matthew Diller") AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000354 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000354 "A symbiosis where one organism is physically contained within another organism (called the 'host')."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000354 "endosymbiosis"@en) -EquivalentClasses(obo:APOLLO_SV_00000354 ObjectIntersectionOf(obo:APOLLO_SV_00000596 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0001025 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000354 ObjectIntersectionOf(obo:APOLLO_SV_00000596 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0001025 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000354 obo:APOLLO_SV_00000596) # Class: obo:APOLLO_SV_00000355 (endosymbiotic parasitism) @@ -5532,7 +5525,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000357 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000357 "A non-intimate agonism in which the harm is fatal."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000357 "Example: lion and gazel"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000357 "predation"@en) -EquivalentClasses(obo:APOLLO_SV_00000357 ObjectIntersectionOf(obo:APOLLO_SV_00000356 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf(obo:APOLLO_SV_00000371 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf(obo:UBERON_0000071 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:OBI_0100026 ObjectAllValuesFrom(obo:RO_0002350 obo:NCBITaxon_33208))))))))) +EquivalentClasses(obo:APOLLO_SV_00000357 ObjectIntersectionOf(obo:APOLLO_SV_00000356 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf(obo:APOLLO_SV_00000371 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf(obo:UBERON_0000071 ObjectSomeValuesFrom(obo:RO_0000057 ObjectIntersectionOf(obo:COB_0000022 ObjectAllValuesFrom(obo:RO_0002350 obo:NCBITaxon_33208))))))))) SubClassOf(obo:APOLLO_SV_00000357 obo:APOLLO_SV_00000356) # Class: obo:APOLLO_SV_00000358 (grazing) @@ -5555,7 +5548,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000359 "facultative endopara AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000359 "An endosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000359 "Example: Strongyloides stercoralis (roundworm) and humans"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000359 "facultative endosymbiotic parasitism"@en) -EquivalentClasses(obo:APOLLO_SV_00000359 ObjectIntersectionOf(obo:APOLLO_SV_00000355 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000359 ObjectIntersectionOf(obo:APOLLO_SV_00000355 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000359 obo:APOLLO_SV_00000355) # Class: obo:APOLLO_SV_00000360 (obligatory endosymbiotic parasitism) @@ -5590,7 +5583,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000362 "facultative endopara AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000362 "An endosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000362 "Example: Naegleria fowleri (brain-eating amoeba) and humans"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000362 "facultative endosymbiotic parasitoidism"@en) -EquivalentClasses(obo:APOLLO_SV_00000362 ObjectIntersectionOf(obo:APOLLO_SV_00000361 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000362 ObjectIntersectionOf(obo:APOLLO_SV_00000361 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000362 obo:APOLLO_SV_00000361) # Class: obo:APOLLO_SV_00000363 (obligatory endosymbiotic parasitoidism) @@ -5613,7 +5606,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000364 "William R. Hogan") AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000364 "endocommensalism"@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000364 "An endosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000364 "endosymbiotic commensalism"@en) -EquivalentClasses(obo:APOLLO_SV_00000364 ObjectIntersectionOf(obo:APOLLO_SV_00000354 ObjectComplementOf(ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:OGMS_0000032 ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026)))) ObjectSomeValuesFrom(obo:BFO_0000051 obo:APOLLO_SV_00000372))) +EquivalentClasses(obo:APOLLO_SV_00000364 ObjectIntersectionOf(obo:APOLLO_SV_00000354 ObjectComplementOf(ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:OGMS_0000032 ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022)))) ObjectSomeValuesFrom(obo:BFO_0000051 obo:APOLLO_SV_00000372))) SubClassOf(obo:APOLLO_SV_00000364 obo:APOLLO_SV_00000354) # Class: obo:APOLLO_SV_00000365 (facultative endosymbiotic commensalism) @@ -5625,7 +5618,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000365 "facultative endocomm AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000365 "An endosymbiotic commensalism that realizes a dispostion of the non-host organism that benefits that is not one of its biological functions."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000365 "Example: Malaria and mosquito vector"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000365 "facultative endosymbiotic commensalism"@en) -EquivalentClasses(obo:APOLLO_SV_00000365 ObjectIntersectionOf(obo:APOLLO_SV_00000364 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000365 ObjectIntersectionOf(obo:APOLLO_SV_00000364 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000365 obo:APOLLO_SV_00000364) # Class: obo:APOLLO_SV_00000366 (obligatory endosymbiotic commensalism) @@ -5637,7 +5630,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000366 "obligatory endocomme AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000366 "An endosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000366 "Example: Passalurus ambiguus (nematode) and rabbits"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000366 "obligatory endosymbiotic commensalism"@en) -EquivalentClasses(obo:APOLLO_SV_00000366 ObjectIntersectionOf(obo:APOLLO_SV_00000364 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:BFO_0000034 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000137 obo:OBI_0100026) ObjectSomeValuesFrom(obo:RO_0000052 obo:UBERON_0000061)))))) +EquivalentClasses(obo:APOLLO_SV_00000366 ObjectIntersectionOf(obo:APOLLO_SV_00000364 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:BFO_0000034 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000137 obo:COB_0000022) ObjectSomeValuesFrom(obo:RO_0000052 obo:UBERON_0000061)))))) SubClassOf(obo:APOLLO_SV_00000366 obo:APOLLO_SV_00000364) # Class: obo:APOLLO_SV_00000367 (endosymbiotic mutualism) @@ -5660,7 +5653,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000368 "facultative endomutu AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000368 "An endosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000368 "Example: Hamiltonella defensa and aphids"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000368 "facultative endosymbiotic mutualism"@en) -EquivalentClasses(obo:APOLLO_SV_00000368 ObjectIntersectionOf(obo:APOLLO_SV_00000367 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026))))) +EquivalentClasses(obo:APOLLO_SV_00000368 ObjectIntersectionOf(obo:APOLLO_SV_00000367 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:APOLLO_SV_00002024 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000372) ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022))))) SubClassOf(obo:APOLLO_SV_00000368 obo:APOLLO_SV_00000367) # Class: obo:APOLLO_SV_00000369 (obligatory endosymbiotic mutualism) @@ -5672,7 +5665,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000369 "obligatory endomutua AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000369 "An endosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000369 "Example: marine worms of genus Riftia and their endosymbiotic bacteria"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000369 "obligatory endosymbiotic mutualism"@en) -EquivalentClasses(obo:APOLLO_SV_00000369 ObjectIntersectionOf(obo:APOLLO_SV_00000367 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:BFO_0000034 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000137 obo:OBI_0100026) ObjectSomeValuesFrom(obo:RO_0000052 obo:UBERON_0000061)))))) +EquivalentClasses(obo:APOLLO_SV_00000369 ObjectIntersectionOf(obo:APOLLO_SV_00000367 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectIntersectionOf(obo:BFO_0000034 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000137 obo:COB_0000022) ObjectSomeValuesFrom(obo:RO_0000052 obo:UBERON_0000061)))))) SubClassOf(obo:APOLLO_SV_00000369 obo:APOLLO_SV_00000367) # Class: obo:APOLLO_SV_00000370 (obsolete homeostasis) @@ -5709,7 +5702,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000373 "Matthew Diller") AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000373 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000373 "An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000373 "parasite"@en) -SubClassOf(obo:APOLLO_SV_00000373 obo:OBI_0100026) +SubClassOf(obo:APOLLO_SV_00000373 obo:COB_0000022) # Class: obo:APOLLO_SV_00000374 (parasitoid) @@ -5718,7 +5711,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000374 "Matthew Diller") AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000374 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000374 "An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000374 "parasitoid"@en) -SubClassOf(obo:APOLLO_SV_00000374 obo:OBI_0100026) +SubClassOf(obo:APOLLO_SV_00000374 obo:COB_0000022) # Class: obo:APOLLO_SV_00000375 (target population definition) @@ -5853,7 +5846,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000389 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000389 "A planned process that realizes a census plan specification."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000389 "Census") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000389 "census taking"@en) -SubClassOf(obo:APOLLO_SV_00000389 obo:OBI_0000011) +SubClassOf(obo:APOLLO_SV_00000389 obo:COB_0000082) # Class: obo:APOLLO_SV_00000390 (Wolbachia vector control strategy) @@ -5938,7 +5931,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000398 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000398 "A data set whose data items are about a host and its participation in an infection and potentially other activities occuring in the same time interval as the infection."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000398 "CaseRecord") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000398 "infection case record"@en) -EquivalentClasses(obo:APOLLO_SV_00000398 ObjectExactCardinality(1 obo:IAO_0000136 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000114)))) +EquivalentClasses(obo:APOLLO_SV_00000398 ObjectExactCardinality(1 obo:IAO_0000136 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000056 obo:APOLLO_SV_00000114)))) SubClassOf(obo:APOLLO_SV_00000398 obo:IAO_0000100) # Class: obo:APOLLO_SV_00000399 (obsolete infection case count) @@ -6001,7 +5994,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000404 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000404 "A disposition inhering in an organism of a particular biological taxon that is realized only by the organism participating in an infection as the reproducing organism inside another organism of a different particular biological taxon."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000404 "The disposition of Influenza A virus H3N2 subtype to infect human beings, the disposition of Plasmodium vivax to infect mosquitos and humans, the disposition of foot and mouth disease virus to infect cloven-hooved animals (sheep, cows, pigs, etc.)."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000404 "infectiousness"@en) -EquivalentClasses(obo:APOLLO_SV_00000404 ObjectIntersectionOf(obo:BFO_0000016 ObjectSomeValuesFrom(obo:RO_0000052 obo:OBI_0100026) ObjectAllValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000114))) +EquivalentClasses(obo:APOLLO_SV_00000404 ObjectIntersectionOf(obo:BFO_0000016 ObjectSomeValuesFrom(obo:RO_0000052 obo:COB_0000022) ObjectAllValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000114))) SubClassOf(obo:APOLLO_SV_00000404 obo:BFO_0000016) # Class: obo:APOLLO_SV_00000405 (potentially infectious contacting) @@ -6034,8 +6027,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000407 "An organism that is AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000407 "William R. Hogan"@en) AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000407 "An organism that has been exposed to a pathogen by coming into close physical proximity with either an infectious host or a contaminated thing."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000407 "contacted organism"@en) -EquivalentClasses(obo:APOLLO_SV_00000407 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000406))) -SubClassOf(obo:APOLLO_SV_00000407 obo:OBI_0100026) +EquivalentClasses(obo:APOLLO_SV_00000407 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:APOLLO_SV_00000406))) +SubClassOf(obo:APOLLO_SV_00000407 obo:COB_0000022) # Class: obo:APOLLO_SV_00000408 (contact definition) @@ -7159,7 +7152,6 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000524 "William R. Hogan"@en AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000524 "It's compiling \"software\" (scare quotes) and not \"source code\" because you can compile Java bytecode to machine code, and Java bytecode is not technically \"source code\". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.)."@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000524 "Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000524 "compiling software"@en) -SubClassOf(obo:APOLLO_SV_00000524 obo:OBI_0000011) # Class: obo:APOLLO_SV_00000525 (compiled software code) @@ -7346,7 +7338,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000545 "Matthew Diller") AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000545 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000545 "A planned process that is the realization of a disease surveillance objective specification."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000545 "disease surveillance"@en) -SubClassOf(obo:APOLLO_SV_00000545 obo:OBI_0000011) +SubClassOf(obo:APOLLO_SV_00000545 obo:COB_0000082) # Class: obo:APOLLO_SV_00000546 (self-initiated travel avoidance behavior) @@ -7572,7 +7564,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000569 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000569 "The total number of diseased individuals in a population at a point in time."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:APOLLO_SV_00000569 "totalCaseCount") AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000569 "total disease cases"@en) -EquivalentClasses(obo:APOLLO_SV_00000569 ObjectIntersectionOf(obo:APOLLO_SV_00000617 ObjectSomeValuesFrom(obo:IAO_0000136 ObjectIntersectionOf(obo:OBI_0100026 ObjectSomeValuesFrom(obo:RO_0000053 obo:OGMS_0000031))) ObjectSomeValuesFrom(obo:OBI_0000312 obo:APOLLO_SV_00000155))) +EquivalentClasses(obo:APOLLO_SV_00000569 ObjectIntersectionOf(obo:APOLLO_SV_00000617 ObjectSomeValuesFrom(obo:IAO_0000136 ObjectIntersectionOf(obo:COB_0000022 ObjectSomeValuesFrom(obo:RO_0000053 obo:OGMS_0000031))) ObjectSomeValuesFrom(obo:OBI_0000312 obo:APOLLO_SV_00000155))) SubClassOf(obo:APOLLO_SV_00000569 obo:APOLLO_SV_00000617) # Class: obo:APOLLO_SV_00000570 (employment status data item) @@ -7665,7 +7657,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000579 "A planned process th AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000579 "Matthew Diller"@en) AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000579 "William R. Hogan"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000579 "infectious disease forecast"@en) -SubClassOf(obo:APOLLO_SV_00000579 obo:OBI_0000011) +SubClassOf(obo:APOLLO_SV_00000579 obo:COB_0000082) # Class: obo:APOLLO_SV_00000580 (infectious disease nowcast) @@ -8377,6 +8369,29 @@ AnnotationAssertion(terms:created obo:APOLLO_SV_00000655 "2026-04-04T19:52:04Z"^ AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000655 "hypothetical scenario"@en) SubClassOf(obo:APOLLO_SV_00000655 obo:APOLLO_SV_00000184) +# Class: obo:APOLLO_SV_00000656 (antibody administration control strategy) + +AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000656 "An individual treatment control strategy that has as part an action specification that (has a concretization that) is realized in an antibody injection process."@en) +AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000656 "William R. Hogan"@en) +AnnotationAssertion(obo:IAO_0000233 obo:APOLLO_SV_00000656 ) +AnnotationAssertion(dc:contributor obo:APOLLO_SV_00000656 "Lucie Contamin") +AnnotationAssertion(terms:created obo:APOLLO_SV_00000656 "2026-07-13T14:13:40Z"^^xsd:dateTime) +AnnotationAssertion(terms:creator obo:APOLLO_SV_00000656 ) +AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000656 "antibody administration control strategy"@en) +SubClassOf(obo:APOLLO_SV_00000656 obo:APOLLO_SV_00000194) + +# Class: obo:APOLLO_SV_00000657 (antibody administration census) + +AnnotationAssertion(obo:IAO_0000115 obo:APOLLO_SV_00000657 "A population treatment census that is about one or more antibody administrations to organisms in a population."@en) +AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000657 "William R. Hogan"@en) +AnnotationAssertion(obo:IAO_0000233 obo:APOLLO_SV_00000657 ) +AnnotationAssertion(dc:contributor obo:APOLLO_SV_00000657 "Lucie Contamin") +AnnotationAssertion(terms:created obo:APOLLO_SV_00000657 "2026-07-13T13:52:47Z"^^xsd:dateTime) +AnnotationAssertion(terms:creator obo:APOLLO_SV_00000657 ) +AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000657 "antibody administration census"@en) +SubClassOf(obo:APOLLO_SV_00000657 obo:APOLLO_SV_00000187) +SubClassOf(obo:APOLLO_SV_00000657 ObjectSomeValuesFrom(obo:IAO_0000136 obo:DRON_00000031)) + # Class: obo:APOLLO_SV_00000793 (epidemic simulator action specification) AnnotationAssertion(obo:IAO_0000111 obo:APOLLO_SV_00000793 "epidemic simulator action specification"@en) @@ -8406,8 +8421,6 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000796 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000796 "data set creation"@en) AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000796 "dataset creation"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000796 "dataset creating"@en) -EquivalentClasses(obo:APOLLO_SV_00000796 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000100))) -SubClassOf(obo:APOLLO_SV_00000796 obo:OBI_0000011) # Class: obo:APOLLO_SV_00000797 (creating a copyright license) @@ -8417,8 +8430,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000797 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000797 "copyright license creation"@en) AnnotationAssertion(rdfs:comment obo:APOLLO_SV_00000797 "Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000797 "creating a copyright license"@en) -EquivalentClasses(obo:APOLLO_SV_00000797 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 obo:APOLLO_SV_00000798))) -SubClassOf(obo:APOLLO_SV_00000797 obo:OBI_0000011) +EquivalentClasses(obo:APOLLO_SV_00000797 ObjectIntersectionOf(obo:COB_0000082 ObjectSomeValuesFrom(obo:OBI_0000299 obo:APOLLO_SV_00000798))) +SubClassOf(obo:APOLLO_SV_00000797 obo:COB_0000082) # Class: obo:APOLLO_SV_00000798 (copyright license) @@ -8572,6 +8585,10 @@ AnnotationAssertion(oboInOwl:id obo:DOID_8469 "DOID:8469") AnnotationAssertion(rdfs:label obo:DOID_8469 "influenza") SubClassOf(obo:DOID_8469 obo:APOLLO_SV_00000239) +# Class: obo:DRON_00000031 (drug administration) + +SubClassOf(obo:DRON_00000031 obo:OGMS_0000090) + # Class: obo:ENVO_00010483 (environmental material) AnnotationAssertion(obo:IAO_0000115 obo:ENVO_00010483 "A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.") @@ -8710,7 +8727,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:ERO_0000657 "environmental genomic analy AnnotationAssertion(obo:IAO_0000119 obo:ERO_0000657 "http://en.wikipedia.org/wiki/Metagenomics") AnnotationAssertion(obo:IAO_0000412 obo:ERO_0000657 "http://purl.obolibrary.org/obo/ero.owl") AnnotationAssertion(rdfs:label obo:ERO_0000657 "metagenomics analysis") -SubClassOf(obo:ERO_0000657 obo:OBI_0000011) +SubClassOf(obo:ERO_0000657 obo:COB_0000082) # Class: obo:FBcv_0000667 (website) @@ -8742,6 +8759,10 @@ AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000372 "William R. Hogan") AnnotationAssertion(obo:IAO_0000600 obo:GEO_000000372 "An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers."@en) AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:GEO_000000372 "Location") +# Class: obo:IDO_0000623 (communicability) + +SubClassOf(obo:IDO_0000623 obo:BFO_0000016) + # Class: obo:NBO_0000034 (sexual activity) AnnotationAssertion(obo:IAO_0000412 obo:NBO_0000034 "http://purl.obolibrary.org/obo/MF.owl") @@ -8760,10 +8781,10 @@ AnnotationAssertion(obo:IAO_0000118 obo:NCBITaxon_10090 "House mouse"@en) AnnotationAssertion(rdfs:label obo:NCBITaxon_10090 "Mus musculus") SubClassOf(obo:NCBITaxon_10090 obo:NCBITaxon_2759) -# Class: obo:NCBITaxon_10239 (Viruses) +# Class: obo:NCBITaxon_10239 (Virus) AnnotationAssertion(rdfs:label obo:NCBITaxon_10239 "Virus"@en) -SubClassOf(obo:NCBITaxon_10239 obo:OBI_0100026) +SubClassOf(obo:NCBITaxon_10239 obo:COB_0000022) # Class: obo:NCBITaxon_10240 (Poxviridae) @@ -10516,7 +10537,7 @@ SubClassOf(obo:NCBITaxon_199306 obo:NCBITaxon_5500) # Class: obo:NCBITaxon_2 (Bacteria) AnnotationAssertion(rdfs:label obo:NCBITaxon_2 "Bacteria"@en) -SubClassOf(obo:NCBITaxon_2 obo:OBI_0100026) +SubClassOf(obo:NCBITaxon_2 obo:COB_0000022) # Class: obo:NCBITaxon_201174 (Actinobacteria ) @@ -10689,7 +10710,7 @@ SubClassOf(obo:NCBITaxon_27319 obo:NCBITaxon_4892) # Class: obo:NCBITaxon_2759 (Eukaryota) AnnotationAssertion(rdfs:label obo:NCBITaxon_2759 "Eukaryota"@en) -SubClassOf(obo:NCBITaxon_2759 obo:OBI_0100026) +SubClassOf(obo:NCBITaxon_2759 obo:COB_0000022) # Class: obo:NCBITaxon_27592 (Bovinae) @@ -13459,492 +13480,14 @@ AnnotationAssertion(obo:IAO_0000412 obo:OAE_0000055 "http://purl.obolibrary.org/ AnnotationAssertion(rdfs:label obo:OAE_0000055 "contraindication"@en) SubClassOf(obo:OAE_0000055 obo:BFO_0000016) -# Class: obo:OBI_0000011 (planned process) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000011 "planned process"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000011 "Injecting mice with a vaccine in order to test its efficacy") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000011 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000011 "A processual entity that realizes a plan which is the concretization of a plan specification."@en) -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000011 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000011 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some - objectives is a planned process.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000011 "Bjoern Peters") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000011 "branch derived") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000011 obo:obi.owl) -AnnotationAssertion(rdfs:label obo:OBI_0000011 "planned process"@en) -EquivalentClasses(obo:OBI_0000011 ObjectSomeValuesFrom(obo:BFO_0000055 ObjectSomeValuesFrom(obo:RO_0000059 ObjectIntersectionOf(obo:IAO_0000104 ObjectSomeValuesFrom(obo:BFO_0000051 obo:IAO_0000005))))) -SubClassOf(obo:OBI_0000011 obo:BFO_0000015) - -# Class: obo:OBI_0000047 (processed material) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000047 "processed material"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000047 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000047 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000047 "Is a material entity that is created or changed during material processing."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000047 "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label obo:OBI_0000047 "processed material"@en) -SubClassOf(obo:OBI_0000047 obo:BFO_0000040) - -# Class: obo:OBI_0000066 (investigation) - -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000066 obo:obi.owl) - -# Class: obo:OBI_0000115 (intervention design) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000115 "intervention design"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000115 "PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study."@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000115 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000115 "An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000115 "Philppe Rocca-Serra"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000115 "OBI branch derived"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000115 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000115 "intervention design"@en) -SubClassOf(obo:OBI_0000115 obo:OBI_0500000) - -# Class: obo:OBI_0000227 (data encoding) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000227 "data encoding"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000227 "storage of measurement results from an assay into a text file, such as"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000227 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000227 "A documenting process to encode an information entity into a digital document"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000227 "PlanAndPlannedProcess Branch"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000227 "OBI branch derived"@en) -AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000227 "We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000227 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000227 "data encoding"@en) -SubClassOf(obo:OBI_0000227 obo:IAO_0000572) - -# Class: obo:OBI_0000245 (organization) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000245 "organization"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000245 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods."@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000245 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000245 "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en) -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000245 "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: - -1) there are organization_member_roles (president, treasurer, branch -editor), with individual persons as bearers - -2) there are organization_roles (employer, owner, vendor, patent holder) - -3) an organization has a charter / rules / bylaws, which specify what roles -there are, how they should be realized, and how to modify the -charter/rules/bylaws themselves. - -It is debatable what the organization itself is (some kind of dependent -continuant or an aggregate of people). This also determines who/what the -bearer of organization_roles' are. My personal favorite is still to define -organization as a kind of 'legal entity', but thinking it through leads to -all kinds of questions that are clearly outside the scope of OBI. - -Interestingly enough, it does not seem to matter much where we place -organization itself, as long as we can subclass it (University, Corporation, -Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, -W3C, University of Oklahoma), and have it play roles. - -This leads to my proposal: We define organization through the statements 1 - -3 above, but without an 'is a' statement for now. We can leave it in its -current place in the is_a hierarchy (material entity) or move it up to -'continuant'. We leave further clarifications to BFO, and close this issue -for now."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Alan Ruttenberg") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Bjoern Peters") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Philippe Rocca-Serra") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Susanna Sansone") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000245 "GROUP: OBI") -AnnotationAssertion(rdfs:label obo:OBI_0000245 "organization"@en) - -# Class: obo:OBI_0000425 (averaging objective) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000425 "averaging objective"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000425 "A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment."@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000425 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000425 "An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000425 "Elisabetta Manduchi") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000425 "James Malone"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000425 "PERSON: Elisabetta Manduchi") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000425 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000425 "averaging objective"@en) -SubClassOf(obo:OBI_0000425 obo:OBI_0200166) - -# Class: obo:OBI_0000471 (study design execution) - -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000471 obo:obi.owl) - -# Class: obo:OBI_0000576 (scattered molecular aggregate) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000576 "scattered molecular aggregate"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000576 "The sodium and chloride ions in a glass of salt water") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000576 obo:IAO_0000123) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000576 "A material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000576 "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000576 "Collective"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000576 "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000576 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000576 "scattered molecular aggregate"@en) -SubClassOf(obo:OBI_0000576 obo:BFO_0000027) - -# Class: obo:OBI_0000658 (data representational model) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000658 "data representational model") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000658 "gene regulatory graph model") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000658 "phylogenetic tree") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000658 "protein interaction network") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000658 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000658 "Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000658 "Melanie Courtot") -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000658 "data structure") -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000658 "data structure specification") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000658 "GROUP: OBI") -AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000658 "2009-02-28: work on this term has been finalized during the OBI workshop winter 2009") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000658 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000658 "data representational model") -SubClassOf(obo:OBI_0000658 obo:IAO_0000033) - -# Class: obo:OBI_0000674 (center value) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000674 "center value"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000674 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000674 "A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000674 "PERSON: James Malone") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000674 "PERSON: Monnie McGee") -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000674 "median") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000674 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:OBI_0000674 "median") -AnnotationAssertion(rdfs:label obo:OBI_0000674 "center value"@en) -SubClassOf(obo:OBI_0000674 obo:IAO_0000027) - -# Class: obo:OBI_0000679 (average value) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000679 "average value") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000679 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000679 "A data item that is produced as the output of an averaging data transformation and represents the average value of the input data."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000679 "PERSON: James Malone") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000679 "PERSON: Monnie McGee") -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000679 "arithmetic mean") -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000679 "false"^^xsd:boolean) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000679 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(obo:IAO_0000600 obo:OBI_0000679 "A data item that is produced as the output of an averaging data transformation and represents the average value of the input data."@en) -AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:OBI_0000679 "mean") -AnnotationAssertion(rdfs:label obo:OBI_0000679 "average value"@en) -EquivalentClasses(obo:OBI_0000679 ObjectIntersectionOf(obo:IAO_0000027 ObjectSomeValuesFrom(obo:OBI_0000312 obo:OBI_0200170))) -SubClassOf(obo:OBI_0000679 obo:IAO_0000027) - -# Class: obo:OBI_0000714 (graph of vertices) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000714 "graph of vertices") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000714 "For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000714 obo:IAO_0000123) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000714 "A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000714 "Bjoern Peters") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000714 "Chris Stoeckert") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000714 "James Malone") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000714 "WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000714 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000714 "graph of vertices") -SubClassOf(obo:OBI_0000714 obo:IAO_0000038) - -# Class: obo:OBI_0000968 (device) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000968 "device") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000968 "A voltmeter is a measurement device which is intended to perform some measure function.") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000968 obo:IAO_0000123) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000968 "A device is a processed material which is designed to perform some function or functions") -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000968 "food should not classify as a device - counter example for using manufacturer and not device. macroscopic only") -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000968 "if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of the definition. device was needed, but couldn't define in Philadelphia. If we decide that in addition to function there are also capabilities for which a device is created we will include these in the definition.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000968 "PERSON: Helen Parkinson") -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000968 "instrument") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000968 "OBI Vancouver workshop 2010") -AnnotationAssertion(rdfs:comment obo:OBI_0000968 "would include reagents") -AnnotationAssertion(rdfs:label obo:OBI_0000968 "device") -SubClassOf(obo:OBI_0000968 obo:OBI_0000047) - -# Class: obo:OBI_0001092 (computer cluster) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001092 "computer cluster") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001092 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001092 "A group of linked computers, working together closely so that in many respects they form a single computer.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001092 "PERSON: Erik Segerdell") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001092 "http://en.wikipedia.org/wiki/Cluster_(computing)") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001092 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0001092 "computer cluster") -SubClassOf(obo:OBI_0001092 obo:OBI_0400107) - # Class: obo:OBI_0001173 (service) -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001173 "service") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001173 "providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony ") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001173 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001173 "A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001173 "Carlo; Matt") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001173 "OBI workshop San Diego 2011") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001173 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0001173 "service") -SubClassOf(obo:OBI_0001173 obo:OBI_0000011) - -# Class: obo:OBI_0001226 (environmental history design) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001226 "environmental history design"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001226 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001226 "A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001226 "Person: Chris Stoeckert, Jie Zheng") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001226 "MO_698 environmental_history_design") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001226 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0001226 "environmental history design"@en) -SubClassOf(obo:OBI_0001226 obo:OBI_0500000) - -# Class: obo:OBI_0001293 (disease state design) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001293 "disease state design"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001293 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001293 "A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001293 "Person: Chris Stoeckert, Jie Zheng") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001293 "MO_902 disease_state_design"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001293 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0001293 "disease state design"@en) -SubClassOf(obo:OBI_0001293 obo:OBI_0500000) - -# Class: obo:OBI_0001454 (pathogenicity design) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001454 "pathogenicity design"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001454 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001454 "A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001454 "Person: Chris Stoeckert, Jie Zheng") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001454 "MO_807 pathogenicity_design"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001454 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0001454 "pathogenicity design"@en) -SubClassOf(obo:OBI_0001454 obo:OBI_0500000) - -# Class: obo:OBI_0001530 (data service) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001530 "data service") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001530 "Data analysis service such statistical abalysis or storage service such data backup.") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001530 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001530 "A service that has some information content entity as input and output.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001530 "PERSON: Carlo Torniai") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001530 "PERSON: Matthew Brush") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001530 "PERSON: Carlo Torniai") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001530 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:comment obo:OBI_0001530 "Information content entity was used as specified input and output since it was more appropriate then data item or dataset.") -AnnotationAssertion(rdfs:label obo:OBI_0001530 "data service") -EquivalentClasses(obo:OBI_0001530 ObjectIntersectionOf(obo:OBI_0001173 ObjectSomeValuesFrom(obo:OBI_0000417 ObjectUnionOf(obo:APOLLO_SV_00000799 ObjectSomeValuesFrom(obo:OBI_0000312 ObjectIntersectionOf(obo:APOLLO_SV_00000524 ObjectSomeValuesFrom(obo:OBI_0000293 obo:APOLLO_SV_00000799))))))) -SubClassOf(obo:OBI_0001530 obo:OBI_0001173) - -# Class: obo:OBI_0001554 (rate measurement datum) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001554 "rate measurement datum") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001554 "The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001554 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001554 "A scalar measurement datum that represents the number of events occuring over a time interval") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001554 "PERSON: Bjoern Peters, Randi Vita") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001554 "IEDB") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001554 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0001554 "rate measurement datum") -SubClassOf(obo:OBI_0001554 obo:IAO_0000032) +SubClassOf(obo:OBI_0001173 obo:COB_0000082) # Class: obo:OBI_0001615 (investigation description) -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001615 "investigation description"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001615 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001615 "A textual entity that describes an investigation."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001615 "Person: Chris Stoeckert, Jie Zheng"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001615 "NIAID GSCID-BRC metadata working group"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001615 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(obo:OBI_0001847 obo:OBI_0001615 "study description") -AnnotationAssertion(obo:OBI_0001886 obo:OBI_0001615 "project description"@en) -AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:OBI_0001615 "investigationDescription") -AnnotationAssertion(dc:source obo:OBI_0001615 "NIAID GSCID-BRC") -AnnotationAssertion(rdfs:label obo:OBI_0001615 "investigation description"@en) SubClassOf(obo:OBI_0001615 obo:IAO_0000300) -# Class: obo:OBI_0001628 (investigation identifier) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001628 "investigation identifier"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001628 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001628 "A CRID symbol used to identify an investigation."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001628 "Person: Chris Stoeckert, Jie Zhneg"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001628 "NIAID GSCID-BRC metadata working group"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001628 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(obo:OBI_0001886 obo:OBI_0001628 "project ID"@en) -AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:OBI_0001628 "investigationLabel") -AnnotationAssertion(dc:source obo:OBI_0001628 "NIAID GSCID-BRC") -AnnotationAssertion(rdfs:label obo:OBI_0001628 "investigation identifier"@en) -SubClassOf(obo:OBI_0001628 obo:IAO_0000577) - -# Class: obo:OBI_0001629 (grant identifier) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001629 "grant identifier"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001629 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001629 "A CRID symbol used to identify a grant."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001629 "Person: Chris Stoeckert, Jie Zheng"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001629 "NIAID GSCID-BRC metadata working group"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001629 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(obo:OBI_0001886 obo:OBI_0001629 "grant ID"@en) -AnnotationAssertion(dc:source obo:OBI_0001629 "NIAID GSCID-BRC") -AnnotationAssertion(rdfs:label obo:OBI_0001629 "grant identifier"@en) -SubClassOf(obo:OBI_0001629 obo:IAO_0020000) - -# Class: obo:OBI_0001958 (systematic review study design) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001958 "systematic review study design") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001958 "Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/ar\\ -ticles/PMC4090399/") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001958 "The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic re\\ -view. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001958 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001958 "A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according \\ -to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were no\\ -t justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001958 "PERSON: Bill Hogan") -AnnotationAssertion(rdfs:label obo:OBI_0001958 "systematic review study design") -SubClassOf(obo:OBI_0001958 obo:OBI_0500000) - -# Class: obo:OBI_0002110 (digital object identifier) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0002110 "digital object identifier"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0002110 "The doi symbol: \"10.1109/5.771073\" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0002110 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0002110 "A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles.") -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0002110 "Discussed on Aug 22, 2016 OBI dev call. Details see tracker: -https://sourceforge.net/p/obi/obi-terms/818/") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0002110 "OBI developers") -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0002110 "DOI") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0002110 "https://en.wikipedia.org/wiki/Digital_object_identifier -https://www.doi.org/") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0002110 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0002110 "digital object identifier"@en) -SubClassOf(obo:OBI_0002110 obo:IAO_0020000) - -# Class: obo:OBI_0100026 (organism) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0100026 "organism"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0100026 obo:IAO_0000121) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0100026 "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) -AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:OBI_0100026 "Individual") -AnnotationAssertion(rdfs:label obo:OBI_0100026 "organism"@en) - -# Class: obo:OBI_0200000 (data transformation) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0200000 "data transformation"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0200000 "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0200000 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200000 "A data transformation is a process which produces output data from input data"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Elisabetta Manduchi"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Helen Parkinson"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "James Malone"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Melanie Courtot"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Philippe Rocca-Serra") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Richard Scheuermann"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Ryan Brinkman"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Tina Hernandez-Boussard"@en) -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0200000 "data analysis"@en) -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0200000 "data processing"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0200000 "Branch editors"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0200000 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0200000 "data transformation"@en) -SubClassOf(obo:OBI_0200000 obo:OBI_0000011) -SubClassOf(obo:OBI_0200000 ObjectSomeValuesFrom(obo:OBI_0000417 obo:OBI_0200166)) - -# Class: obo:OBI_0200166 (data transformation objective) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0200166 "data transformation objective"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0200166 "normalize objective"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0200166 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200166 "A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200166 "James Malone"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0200166 "PERSON: James Malone"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0200166 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0200166 "data transformation objective"@en) -SubClassOf(obo:OBI_0200166 obo:IAO_0000005) - -# Class: obo:OBI_0200170 (averaging data transformation) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0200170 "averaging data transformation"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0200170 obo:IAO_0000123) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200170 "An averaging data transformation is a data transformation that has objective averaging."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200170 "James Malone") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0200170 "PERSON: James Malone"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0200170 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0200170 "averaging data transformation"@en) -EquivalentClasses(obo:OBI_0200170 ObjectUnionOf(ObjectSomeValuesFrom(obo:OBI_0000299 obo:OBI_0000679) ObjectSomeValuesFrom(obo:OBI_0000417 obo:OBI_0000425))) -SubClassOf(obo:OBI_0200170 obo:OBI_0200000) - -# Class: obo:OBI_0300311 (observation design) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0300311 "observation design"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0300311 "PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study."@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0300311 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0300311 "observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0300311 "Philippe Rocca-Serra"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0300311 "OBI branch derived"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0300311 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0300311 "observation design"@en) -SubClassOf(obo:OBI_0300311 obo:OBI_0500000) - -# Class: obo:OBI_0302867 (predicted data item) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0302867 "predicted data item") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0302867 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0302867 "A data item that was generated on the basis of a calculation or logical reasoning"@en) -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0302867 "BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. ") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0302867 "Philippe Rocca-Serra; Bjoern Peters") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0302867 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:comment obo:OBI_0302867 "APOLLO DEVELOPERS: We need to check whether OBI changes the label and the hierarchical place of this class."@en) -AnnotationAssertion(rdfs:label obo:OBI_0302867 "calculated datum"@en) -AnnotationAssertion(rdfs:label obo:OBI_0302867 "predicted data item"@en) -SubClassOf(obo:OBI_0302867 obo:IAO_0000109) - -# Class: obo:OBI_0302914 (digital curation) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0302914 "digital curation"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0302914 "PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44."@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0302914 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0302914 "Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0302914 "Philippe Rocca-Serra") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0302914 "wikipedia") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0302914 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0302914 "digital curation"@en) -SubClassOf(obo:OBI_0302914 obo:IAO_0000572) - -# Class: obo:OBI_0400107 (computer) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0400107 "computer"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0400107 "Apple PowerBook, Dell OptiPlex"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0400107 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0400107 "A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0400107 "Melanie Courtot"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0400107 "Trish Whetzel"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0400107 "http://en.wikipedia.org/wiki/Computer"@en) -AnnotationAssertion(rdfs:label obo:OBI_0400107 "computer"@en) -SubClassOf(obo:OBI_0400107 obo:OBI_0000968) - -# Class: obo:OBI_0500000 (study design) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0500000 "study design"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0500000 "A matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design."@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0500000 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0500000 "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.") -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0500000 "Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0500000 "PERSON: Chris Stoeckert") -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0500000 "experimental design"@en) -AnnotationAssertion(obo:IAO_0000232 obo:OBI_0500000 "rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol."@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0500000 obo:obi.owl) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0500000 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0500000 "study design"@en) -SubClassOf(obo:OBI_0500000 obo:IAO_0000104) - -# Class: obo:OBI_0500020 (time series design) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0500020 "time series design"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0500020 "PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources."@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0500020 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0500020 "Groups of assays that are related as part of a time series."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0500020 "Philippe Rocca-Serra on behalf of MO"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0500020 "MO_887"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0500020 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0500020 "time series design"@en) -SubClassOf(obo:OBI_0500020 obo:OBI_0500000) - # Class: obo:OBIws_0000050 (software execution) AnnotationAssertion(obo:IAO_0000115 obo:OBIws_0000050 "A planned process that realizes the concretization of a software."@en) @@ -13953,7 +13496,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:OBIws_0000050 "operation") AnnotationAssertion(obo:IAO_0000119 obo:OBIws_0000050 "ITPPR") AnnotationAssertion(obo:IAO_0000412 obo:OBIws_0000050 "http://purl.obolibrary.org/obo/OBIws.owl") AnnotationAssertion(rdfs:label obo:OBIws_0000050 "software execution"@en) -SubClassOf(obo:OBIws_0000050 obo:OBI_0000011) +SubClassOf(obo:OBIws_0000050 obo:COB_0000082) # Class: obo:OBIws_0000104 (web service execution) @@ -14016,7 +13559,7 @@ AnnotationAssertion(oboInOwl:inSubset obo:PATO_0000051 pato:attribute_slim) AnnotationAssertion(rdfs:label obo:PATO_0000051 "morphology") SubClassOf(obo:PATO_0000051 obo:PATO_0001241) -# Class: obo:PATO_0000117 (size) +# Class: obo:PATO_0000117 (obo:PATO_0000117) SubClassOf(obo:PATO_0000117 obo:PATO_0000051) @@ -14390,8 +13933,8 @@ AnnotationAssertion(obo:IAO_0000412 obo:VO_0000001 "http://purl.obolibrary.org/o AnnotationAssertion(apollo_sv:APOLLO_SV_0000040 obo:VO_0000001 "Vaccine") AnnotationAssertion(rdfs:label obo:VO_0000001 "vaccine") AnnotationAssertion(rdfs:seeAlso obo:VO_0000001 "MeSH: D014612") -EquivalentClasses(obo:VO_0000001 ObjectIntersectionOf(obo:OBI_0000047 ObjectSomeValuesFrom(obo:OBI_0000312 obo:VO_0000590) ObjectSomeValuesFrom(obo:RO_0000053 ObjectIntersectionOf(obo:VO_0000278 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000142))))) -SubClassOf(obo:VO_0000001 obo:OBI_0000047) +EquivalentClasses(obo:VO_0000001 ObjectIntersectionOf(obo:COB_0000026 ObjectSomeValuesFrom(obo:OBI_0000312 obo:VO_0000590) ObjectSomeValuesFrom(obo:RO_0000053 ObjectIntersectionOf(obo:VO_0000278 ObjectSomeValuesFrom(obo:BFO_0000054 obo:APOLLO_SV_00000142))))) +SubClassOf(obo:VO_0000001 obo:COB_0000026) # Class: obo:VO_0000207 (vaccine contraindication) @@ -14420,7 +13963,7 @@ AnnotationAssertion(obo:IAO_0000118 obo:VO_0000590 "vaccine generation") AnnotationAssertion(obo:IAO_0000118 obo:VO_0000590 "vaccine production") AnnotationAssertion(obo:IAO_0000412 obo:VO_0000590 "http://purl.obolibrary.org/obo/vo.owl") AnnotationAssertion(rdfs:label obo:VO_0000590 "vaccine preparation") -SubClassOf(obo:VO_0000590 obo:OBI_0000011) +SubClassOf(obo:VO_0000590 obo:COB_0000082) # Class: (obsolete specificity of case detection) @@ -14467,7 +14010,7 @@ AnnotationAssertion(obo:IAO_0000115 "Geno AnnotationAssertion(obo:IAO_0000117 "James Malone") AnnotationAssertion(rdfs:label "genomic data") SubClassOf( obo:IAO_0000100) -SubClassOf( ObjectSomeValuesFrom(obo:IAO_0000136 obo:OBI_0100026)) +SubClassOf( ObjectSomeValuesFrom(obo:IAO_0000136 obo:COB_0000022)) # Class: oboInOwl:ObsoleteClass (Obsolete Class) @@ -14496,6 +14039,7 @@ ClassAssertion(obo:UO_0000003 obo:UO_0000034) # Individual: (William R. Hogan) AnnotationAssertion(terms:created "2026-04-04T19:54:38Z"^^xsd:dateTime) +AnnotationAssertion(terms:creator ) AnnotationAssertion(rdfs:label "William R. Hogan"@en) ClassAssertion(obo:NCBITaxon_9606 ) diff --git a/src/ontology/apollo_sv-idranges.owl b/src/ontology/apollo_sv-idranges.owl index 33fedbc..717affd 100644 --- a/src/ontology/apollo_sv-idranges.owl +++ b/src/ontology/apollo_sv-idranges.owl @@ -16,7 +16,7 @@ Ontology: Annotations: idsfor: "APOLLO_SV", - idprefix: "http://purl.obolibrary.org/obo/APOLLOSV_", + idprefix: "http://purl.obolibrary.org/obo/APOLLO_SV_", iddigits: 8 AnnotationProperty: idprefix: diff --git a/src/ontology/apollo_sv-odk.yaml b/src/ontology/apollo_sv-odk.yaml index 7995332..3832652 100644 --- a/src/ontology/apollo_sv-odk.yaml +++ b/src/ontology/apollo_sv-odk.yaml @@ -24,11 +24,13 @@ import_group: module_type: slme slme_individuals: exclude - id: geo + make_base: true mirror_from: http://purl.obolibrary.org/obo/geo/dev/geo.owl - module_type: mirror - id: ido - module_type: slme - slme_individuals: exclude + module_type: filter + make_base: true + base_iris: + - http://purl.obolibrary.org/obo/IDO_ - id: mf module_type: slme slme_individuals: exclude @@ -60,6 +62,13 @@ import_group: mirror_from: http://humanbehaviourchange.org/ontology/bcio.owl base_iris: - http://humanbehaviourchange.org/ontology/BCIO_ + - id: obi + module_type: filter + make_base: true + base_iris: + - http://purl.obolibrary.org/obo/COB_ + - http://purl.obolibrary.org/obo/IAO_ + - http://purl.obolibrary.org/obo/OBI_ use_custom_import_module: TRUE robot_java_args: '-Xmx16G' custom_makefile_header: | diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 496f2fd..0b2d953 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -12,6 +12,7 @@ + diff --git a/src/ontology/imports/bcio_import.owl b/src/ontology/imports/bcio_import.owl index d869fc3..84abc44 100644 --- a/src/ontology/imports/bcio_import.owl +++ b/src/ontology/imports/bcio_import.owl @@ -8,21 +8,24 @@ Prefix(xml:=) Prefix(xsd:=) Prefix(foaf:=) Prefix(rdfs:=) +Prefix(skos:=) Prefix(sssom:=) Prefix(terms:=) Prefix(schema:=) Prefix(Property:=) +Prefix(metadata:=) Prefix(oboInOwl:=) Prefix(owlready_ontology:=) Ontology( - -Annotation(dc:source ) -Annotation(owl:versionInfo "2026-03-13") + +Annotation(dc:source ) +Annotation(owl:versionInfo "2026-07-19") Declaration(Class()) Declaration(Class()) +Declaration(Class(obo:OGMS_0000060)) Declaration(AnnotationProperty(obo:IAO_0000112)) Declaration(AnnotationProperty(obo:IAO_0000114)) Declaration(AnnotationProperty(obo:IAO_0000115)) @@ -67,6 +70,7 @@ Every behaviour is associated with mental processes, but not every mental proces 'A 'striated muscle' can defined as 'a type of contractile tissue that is marked by transverse striations") AnnotationAssertion(rdfs:label "individual human behaviour") +SubClassOf( obo:OGMS_0000060) ) \ No newline at end of file diff --git a/src/ontology/imports/dron_import.owl b/src/ontology/imports/dron_import.owl index b0d966b..dadb1d1 100644 --- a/src/ontology/imports/dron_import.owl +++ b/src/ontology/imports/dron_import.owl @@ -21,17 +21,20 @@ Prefix(oboInOwl:=) Ontology( - -Annotation(dc:source ) -Annotation(owl:versionInfo "2026-03-13") + +Annotation(dc:source ) +Annotation(owl:versionInfo "2026-07-19") Declaration(Class(obo:BFO_0000040)) Declaration(Class(obo:DRON_00000005)) +Declaration(Class(obo:DRON_00000031)) Declaration(Class(obo:DRON_00000074)) +Declaration(AnnotationProperty(obo:IAO_0000111)) Declaration(AnnotationProperty(obo:IAO_0000115)) Declaration(AnnotationProperty(obo:IAO_0000117)) Declaration(AnnotationProperty(dc:source)) Declaration(AnnotationProperty(dcterms:contributor)) +Declaration(AnnotationProperty(dcterms:creator)) ############################ @@ -42,16 +45,25 @@ Declaration(AnnotationProperty(dcterms:contributor)) AnnotationAssertion(obo:IAO_0000115 obo:DRON_00000005 "A drug product that is bearer of a clinical drug role."@en) AnnotationAssertion(obo:IAO_0000117 obo:DRON_00000005 "William Hogan"@en) +AnnotationAssertion(dcterms:creator obo:DRON_00000005 "https://orcid.org/0000-0002-9881-1017"^^xsd:anyURI) AnnotationAssertion(rdfs:comment obo:DRON_00000005 "We changed the label to 'clinical drug product' because it was clear that the part of the definition re: bearer of a \"clinical drug role\" made it such. Other drugs don't have clinical drug roles, especially illicit ones. Therefore we changed the label here, as well as the subClassOf. Now it is subClassOf \"drug product\", which also required changing the definition here."@en) AnnotationAssertion(rdfs:label obo:DRON_00000005 "clinical drug product"@en) SubClassOf(obo:DRON_00000005 obo:DRON_00000074) +# Class: obo:DRON_00000031 (drug administration) + +AnnotationAssertion(obo:IAO_0000111 obo:DRON_00000031 "administration of a drug product to an organism"@en) +AnnotationAssertion(obo:IAO_0000115 obo:DRON_00000031 "A treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:DRON_00000031 "William R. Hogan"@en) +AnnotationAssertion(rdfs:label obo:DRON_00000031 "drug administration"@en) + # Class: obo:DRON_00000074 (drug product) AnnotationAssertion(obo:IAO_0000115 obo:DRON_00000074 "A material entity that (1) contains at least one scattered molecular aggregate as part and (2) is intended, when administered to an organism, to produce some therapeutic and/or psychoactive effect."@en) AnnotationAssertion(obo:IAO_0000117 obo:DRON_00000074 "William R. Hogan"@en) AnnotationAssertion(dcterms:contributor obo:DRON_00000074 ) AnnotationAssertion(dcterms:contributor obo:DRON_00000074 ) +AnnotationAssertion(dcterms:creator obo:DRON_00000074 "http://orcid.org/0000-0002-9881-1017") AnnotationAssertion(rdfs:comment obo:DRON_00000074 "The \"intention\" part is important because of situations, such as that with phenylephrine, where it was not effective for the labeled use. Even when a drug is proven effective for a particular indication, it might not be therapeutic for every indivdiual to whom it is administered."@en) AnnotationAssertion(rdfs:comment obo:DRON_00000074 "The psychoactive effect is added for illicit drugs such as crack cocaine."@en) AnnotationAssertion(rdfs:comment obo:DRON_00000074 "We are including prophylactic and diagnostic effects / usage under the more general heading of 'therapeutic'."@en) diff --git a/src/ontology/imports/dron_terms.txt b/src/ontology/imports/dron_terms.txt index 4a25dc8..8d8d2d1 100644 --- a/src/ontology/imports/dron_terms.txt +++ b/src/ontology/imports/dron_terms.txt @@ -1,3 +1,4 @@ http://purl.obolibrary.org/obo/DRON_00000005 http://purl.obolibrary.org/obo/DRON_00000074 +http://purl.obolibrary.org/obo/DRON_00000031 diff --git a/src/ontology/imports/external_import.owl b/src/ontology/imports/external_import.owl index e4ab54c..5b9b5af 100644 --- a/src/ontology/imports/external_import.owl +++ b/src/ontology/imports/external_import.owl @@ -9,6 +9,10 @@ Prefix(rdfs:=) Ontology( Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class(owl:Thing)) ) \ No newline at end of file diff --git a/src/ontology/imports/geo_import.owl b/src/ontology/imports/geo_import.owl index ec83297..db4eead 100644 --- a/src/ontology/imports/geo_import.owl +++ b/src/ontology/imports/geo_import.owl @@ -13,635 +13,45 @@ Prefix(oboInOwl:=) Ontology( - -Import() -Import() -Annotation(owl:versionInfo "2026-03-13") + +Annotation(owl:versionInfo "2026-07-19") -Declaration(Class(obo:BFO_0000004)) -Declaration(Class(obo:BFO_0000027)) Declaration(Class(obo:BFO_0000040)) -Declaration(Class(obo:GEO_000000001)) -Declaration(Class(obo:GEO_000000002)) -Declaration(Class(obo:GEO_000000003)) Declaration(Class(obo:GEO_000000004)) Declaration(Class(obo:GEO_000000005)) Declaration(Class(obo:GEO_000000006)) -Declaration(Class(obo:GEO_000000007)) -Declaration(Class(obo:GEO_000000008)) -Declaration(Class(obo:GEO_000000334)) -Declaration(Class(obo:GEO_000000335)) -Declaration(Class(obo:GEO_000000337)) -Declaration(Class(obo:GEO_000000357)) -Declaration(Class(obo:GEO_000000369)) Declaration(Class(obo:GEO_000000370)) Declaration(Class(obo:GEO_000000371)) Declaration(Class(obo:GEO_000000372)) -Declaration(Class(obo:GEO_000000373)) -Declaration(Class(obo:GEO_000000374)) -Declaration(Class(obo:GEO_000000375)) -Declaration(Class(obo:GEO_000000376)) -Declaration(Class(obo:GEO_000000377)) -Declaration(Class(obo:GEO_000000378)) -Declaration(Class(obo:GEO_000000390)) Declaration(Class(obo:GEO_000000391)) Declaration(Class(obo:GEO_000000392)) Declaration(Class(obo:GEO_000000393)) Declaration(Class(obo:GEO_000000395)) Declaration(Class(obo:GEO_000000396)) Declaration(Class(obo:GEO_000000400)) -Declaration(Class(obo:GEO_000000401)) -Declaration(Class(obo:GEO_000000402)) -Declaration(Class(obo:GEO_000000403)) -Declaration(Class(obo:GEO_000000404)) -Declaration(Class(obo:GEO_000000787)) Declaration(Class(obo:GEO_000000788)) -Declaration(Class(obo:GEO_000000789)) Declaration(Class(obo:GEO_000000797)) -Declaration(Class(obo:IAO_0000003)) -Declaration(Class(obo:IAO_0000009)) -Declaration(Class(obo:IAO_0000032)) -Declaration(Class(obo:IAO_0000109)) +Declaration(Class(obo:IAO_0000030)) Declaration(Class(obo:OBI_0000245)) -Declaration(Class(obo:OBI_0001620)) -Declaration(Class(obo:OBI_0001621)) -Declaration(Class(obo:OBI_0001931)) -Declaration(Class(obo:OBI_0001933)) -Declaration(Class(obo:PATO_0000117)) -Declaration(Class(obo:PATO_0001241)) -Declaration(Class(obo:PATO_0001323)) -Declaration(Class(obo:PATO_0001709)) -Declaration(Class(obo:UO_0000047)) -Declaration(Class()) -Declaration(Class(oboInOwl:ObsoleteClass)) -Declaration(ObjectProperty(obo:BFO_0000075)) -Declaration(ObjectProperty(obo:BFO_0000083)) -Declaration(ObjectProperty(obo:BFO_0000110)) -Declaration(ObjectProperty(obo:BFO_0000111)) -Declaration(ObjectProperty(obo:BFO_0000123)) -Declaration(ObjectProperty(obo:BFO_0000137)) -Declaration(ObjectProperty(obo:BFO_0000177)) -Declaration(ObjectProperty(obo:BFO_0000187)) -Declaration(ObjectProperty(obo:GEO_000000328)) -Declaration(ObjectProperty(obo:GEO_000000329)) -Declaration(ObjectProperty(obo:GEO_000000336)) -Declaration(ObjectProperty(obo:IAO_0000039)) -Declaration(ObjectProperty(obo:IAO_0000136)) -Declaration(ObjectProperty(obo:OBI_0000293)) -Declaration(ObjectProperty(obo:OBI_0000295)) -Declaration(ObjectProperty(obo:OBI_0000299)) -Declaration(ObjectProperty(obo:OBI_0000312)) -Declaration(ObjectProperty(obo:OBI_0001938)) -Declaration(ObjectProperty(obo:RO_0000056)) -Declaration(ObjectProperty(obo:RO_0000057)) -Declaration(DataProperty(obo:IAO_0000004)) Declaration(NamedIndividual(obo:GEO_000000790)) -Declaration(NamedIndividual(obo:GEO_000000791)) -Declaration(NamedIndividual(obo:GEO_000000796)) -Declaration(NamedIndividual(obo:UO_0000080)) -Declaration(AnnotationProperty(obo:GEO_000000009)) -Declaration(AnnotationProperty(obo:GEO_000000010)) -Declaration(AnnotationProperty(obo:GEO_000000011)) -Declaration(AnnotationProperty(obo:GEO_000000021)) -Declaration(AnnotationProperty(obo:GEO_000000022)) -Declaration(AnnotationProperty(obo:GEO_000000023)) -Declaration(AnnotationProperty(obo:GEO_000000358)) -Declaration(AnnotationProperty(obo:GEO_000000359)) -Declaration(AnnotationProperty(obo:GEO_000035330)) -Declaration(AnnotationProperty(obo:GEO_000035331)) -Declaration(AnnotationProperty(obo:GEO_000035332)) -Declaration(AnnotationProperty(obo:GEO_000035333)) -Declaration(AnnotationProperty(obo:GEO_000035334)) -Declaration(AnnotationProperty(obo:OBI_0001886)) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(obo:IAO_0000111)) +Declaration(AnnotationProperty(obo:IAO_0000115)) +Declaration(AnnotationProperty(obo:IAO_0000117)) +Declaration(AnnotationProperty(obo:IAO_0000118)) +Declaration(AnnotationProperty(obo:IAO_0000119)) Declaration(AnnotationProperty(dc:contributor)) -Declaration(AnnotationProperty(oboInOwl:SubsetProperty)) -Declaration(AnnotationProperty(oboInOwl:created_by)) -Declaration(AnnotationProperty(oboInOwl:hasAlternativeId)) -Declaration(AnnotationProperty(oboInOwl:hasDbXref)) -Declaration(AnnotationProperty(oboInOwl:hasDefinition)) -Declaration(AnnotationProperty(oboInOwl:hasExactSynonym)) -Declaration(AnnotationProperty(oboInOwl:hasNarrowSynonym)) -Declaration(AnnotationProperty(oboInOwl:hasOBONamespace)) -Declaration(AnnotationProperty(oboInOwl:id)) -Declaration(AnnotationProperty(oboInOwl:inSubset)) -############################ -# Annotation Properties -############################ - -# Annotation Property: obo:BFO_0000179 (BFO OWL specification label) - -AnnotationAssertion(rdfs:label obo:BFO_0000179 "BFO OWL specification label"@en) - -# Annotation Property: obo:BFO_0000180 (BFO CLIF specification label) - -AnnotationAssertion(rdfs:label obo:BFO_0000180 "BFO CLIF specification label"@en) - -# Annotation Property: obo:GEO_000000009 (US State Two Digit Identifier) - -AnnotationAssertion(rdfs:label obo:GEO_000000009 "US State Two Digit Identifier"@en) - -# Annotation Property: obo:GEO_000000010 (US State Two Letter Abbreviation) - -AnnotationAssertion(rdfs:label obo:GEO_000000010 "US State Two Letter Abbreviation"@en) - -# Annotation Property: obo:GEO_000000011 (US State Ens Identifier) - -AnnotationAssertion(rdfs:label obo:GEO_000000011 "US State Ens Identifier"@en) - -# Annotation Property: obo:GEO_000000021 (UN Numerical Code) - -AnnotationAssertion(rdfs:label obo:GEO_000000021 "UN Numerical Code"@en) - -# Annotation Property: obo:GEO_000000022 (ISO 3166-1-alpha-3 code) - -AnnotationAssertion(rdfs:label obo:GEO_000000022 "ISO 3166-1-alpha-3 code"@en) - -# Annotation Property: obo:GEO_000000023 (ISO 3166-1-alpha-2 code) - -AnnotationAssertion(rdfs:label obo:GEO_000000023 "ISO 3166-1-alpha-2 code"@en) - -# Annotation Property: obo:GEO_000000358 (Proposed Apollo Location Code) - -AnnotationAssertion(rdfs:label obo:GEO_000000358 "Proposed Apollo Location Code"@en) - -# Annotation Property: obo:GEO_000000359 (ISO 3166-2 code) - -AnnotationAssertion(rdfs:label obo:GEO_000000359 "ISO 3166-2 code"@en) - -# Annotation Property: obo:GEO_000035330 (geonameid) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000035330 "geonameid"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000035330 "integer id of record in geonames database"@en) -AnnotationAssertion(rdfs:label obo:GEO_000035330 "geonameid") - -# Annotation Property: obo:GEO_000035331 (admin1 code) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000035331 "geonames admin1 code"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000035331 "fipscode (subject to change to iso code), see exceptions below, see file admin1Codes.txt for display names of this code; varchar(20)"@en) -AnnotationAssertion(rdfs:label obo:GEO_000035331 "admin1 code") - -# Annotation Property: obo:GEO_000035332 (admin2 code) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000035332 "geonames admin2 code"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000035332 "code for the second administrative division, a county in the US, see file admin2Codes.txt; varchar(80)"@en) -AnnotationAssertion(rdfs:label obo:GEO_000035332 "admin2 code") - -# Annotation Property: obo:GEO_000035333 (admin3 code) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000035333 "geonames admin3 code"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000035333 "code for third level administrative division, varchar(20)"@en) -AnnotationAssertion(rdfs:label obo:GEO_000035333 "admin3 code") - -# Annotation Property: obo:GEO_000035334 (admin4 code) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000035334 "geonames admin4 code"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000035334 "code for fourth level administrative division, varchar(20)"@en) -AnnotationAssertion(rdfs:label obo:GEO_000035334 "admin4 code") - -# Annotation Property: obo:IAO_0000111 (editor preferred term) - -AnnotationAssertion(rdfs:label obo:IAO_0000111 "editor preferred label"@en) -AnnotationAssertion(rdfs:label obo:IAO_0000111 "editor preferred term") -AnnotationAssertion(rdfs:label obo:IAO_0000111 "editor preferred term"@en) -AnnotationAssertion(rdfs:label obo:IAO_0000111 "editor preferred term~editor preferred label") - -# Annotation Property: obo:IAO_0000112 (example of usage) - -AnnotationAssertion(rdfs:label obo:IAO_0000112 "example of usage"@en) - -# Annotation Property: obo:IAO_0000114 (has curation status) - -AnnotationAssertion(rdfs:label obo:IAO_0000114 "has curation status"@en) - -# Annotation Property: obo:IAO_0000115 (definition) - -AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition") -AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition"@en) -AnnotationAssertion(rdfs:label obo:IAO_0000115 "textual definition") - -# Annotation Property: obo:IAO_0000116 (editor note) - -AnnotationAssertion(rdfs:label obo:IAO_0000116 "editor note"@en) - -# Annotation Property: obo:IAO_0000117 (term editor) - -AnnotationAssertion(rdfs:label obo:IAO_0000117 "definition editor"@en) -AnnotationAssertion(rdfs:label obo:IAO_0000117 "term editor"@en) - -# Annotation Property: obo:IAO_0000118 (alternative label) - -AnnotationAssertion(rdfs:label obo:IAO_0000118 "alternative term"@en) - -# Annotation Property: obo:IAO_0000119 (definition source) - -AnnotationAssertion(rdfs:label obo:IAO_0000119 "definition source"@en) - -# Annotation Property: obo:IAO_0000232 (curator note) - -AnnotationAssertion(rdfs:label obo:IAO_0000232 "curator note"@en) - -# Annotation Property: obo:IAO_0000412 (imported from) - -AnnotationAssertion(rdfs:label obo:IAO_0000412 "imported from"@en) - -# Annotation Property: obo:IAO_0000600 (elucidation) - -AnnotationAssertion(rdfs:label obo:IAO_0000600 "elucidation"@en) - -# Annotation Property: obo:IAO_0000601 (has associated axiom(nl)) - -AnnotationAssertion(rdfs:label obo:IAO_0000601 "has associated axiom(nl)"@en) - -# Annotation Property: obo:IAO_0000602 (has associated axiom(fol)) - -AnnotationAssertion(rdfs:label obo:IAO_0000602 "has associated axiom(fol)"@en) - -# Annotation Property: obo:OBI_0001886 (NIAID GSCID-BRC alternative term) - -AnnotationAssertion(rdfs:label obo:OBI_0001886 "NIAID GSCID-BRC alternative term"@en) - -# Annotation Property: () - -SubAnnotationPropertyOf( oboInOwl:SubsetProperty) - -# Annotation Property: () - -SubAnnotationPropertyOf( oboInOwl:SubsetProperty) - -# Annotation Property: () - -SubAnnotationPropertyOf( oboInOwl:SubsetProperty) - -# Annotation Property: () - -SubAnnotationPropertyOf( oboInOwl:SubsetProperty) - -# Annotation Property: dc:source (Source) - -AnnotationAssertion(rdfs:label dc:source "Source") -AnnotationAssertion(rdfs:label dc:source "Source"@en-us) - -# Annotation Property: oboInOwl:hasAlternativeId (has_alternative_id) - -AnnotationAssertion(rdfs:label oboInOwl:hasAlternativeId "has_alternative_id") - -# Annotation Property: oboInOwl:hasDbXref (database_cross_reference) - -AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference") - -# Annotation Property: oboInOwl:hasDefinition (has_definition) - -AnnotationAssertion(rdfs:label oboInOwl:hasDefinition "has_definition"@en) - -# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) - -AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym") - -# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym) - -AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") - -# Annotation Property: oboInOwl:hasOBONamespace (has_obo_namespace) - -AnnotationAssertion(rdfs:label oboInOwl:hasOBONamespace "has_obo_namespace") - -# Annotation Property: oboInOwl:inSubset (in_subset) - -AnnotationAssertion(rdfs:label oboInOwl:inSubset "in_subset") - -# Annotation Property: rdfs:label (label) - -AnnotationAssertion(rdfs:label rdfs:label "label") - - -############################ -# Object Properties -############################ - -# Object Property: obo:BFO_0000075 (is aggregate of) - -AnnotationAssertion(obo:IAO_0000118 obo:BFO_0000075 "aggregate of"@en) -AnnotationAssertion(obo:IAO_0000118 obo:BFO_0000075 "aggregate_of"@en) -AnnotationAssertion(obo:IAO_0000412 obo:BFO_0000075 "http://purl.obolibrary.org/obo/omrse.owl") -AnnotationAssertion(rdfs:label obo:BFO_0000075 "is aggregate of"@en) -SubObjectPropertyOf(obo:BFO_0000075 owl:topObjectProperty) -InverseObjectProperties(obo:BFO_0000075 obo:GEO_000000328) - -# Object Property: obo:BFO_0000083 (occupies spatial region at some time) - -AnnotationAssertion(obo:BFO_0000179 obo:BFO_0000083 "located-at-r_st") -AnnotationAssertion(obo:BFO_0000180 obo:BFO_0000083 "occupiesSpatialRegionAt") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000083 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000083 "BFO2 Reference: independent continuant") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000083 "BFO2 Reference: spatial region") -AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000083 "b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])"@en) -AnnotationAssertion(obo:IAO_0000601 obo:BFO_0000083 "every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])"@en) -AnnotationAssertion(obo:IAO_0000601 obo:BFO_0000083 "if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])"@en) -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000083 "(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] ") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000083 "(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] ") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000083 "(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] ") -AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000083 obo:bfo.owl) -AnnotationAssertion(rdfs:label obo:BFO_0000083 "occupies spatial region at some time"@en) -InverseObjectProperties(obo:BFO_0000083 obo:BFO_0000123) -ObjectPropertyDomain(obo:BFO_0000083 obo:BFO_0000004) -ObjectPropertyRange(obo:BFO_0000083 obo:BFO_0000006) - -# Object Property: obo:BFO_0000110 (has continuant part at all times) - -AnnotationAssertion(obo:BFO_0000179 obo:BFO_0000110 "c-has-part_at") -AnnotationAssertion(obo:BFO_0000180 obo:BFO_0000110 "hasContinuantPartAt") -AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000110 "[copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)") -AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000110 "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])"@en) -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000110 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000110 "[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'") -AnnotationAssertion(obo:IAO_0000412 obo:BFO_0000110 "http://purl.obolibrary.org/obo/bfo.owl") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000110 "(iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] ") -AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000110 obo:bfo.owl) -AnnotationAssertion(rdfs:label obo:BFO_0000110 "has continuant part at all times"@en) -SubObjectPropertyOf(obo:BFO_0000110 owl:topObjectProperty) - -# Object Property: obo:BFO_0000111 (has proper continuant part at all times) - -AnnotationAssertion(obo:BFO_0000179 obo:BFO_0000111 "c-has-ppart_at") -AnnotationAssertion(obo:BFO_0000180 obo:BFO_0000111 "hasProperContinuantPartAt") -AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000111 "b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001"@en) -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000111 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'.") -AnnotationAssertion(obo:IAO_0000412 obo:BFO_0000111 "http://purl.obolibrary.org/obo/bfo.owl") -AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000111 obo:bfo.owl) -AnnotationAssertion(rdfs:label obo:BFO_0000111 "has proper continuant part at all times"@en) -SubObjectPropertyOf(obo:BFO_0000111 obo:BFO_0000110) - -# Object Property: obo:BFO_0000123 (has spatial occupant at some time) - -AnnotationAssertion(obo:BFO_0000179 obo:BFO_0000123 "r-location-of_st") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000123 "[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000123 "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000123 "[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region") -AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000123 "[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])") -AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000123 obo:bfo.owl) -AnnotationAssertion(rdfs:label obo:BFO_0000123 "has spatial occupant at some time"@en) -ObjectPropertyDomain(obo:BFO_0000123 obo:BFO_0000006) -ObjectPropertyRange(obo:BFO_0000123 obo:BFO_0000004) - -# Object Property: obo:BFO_0000137 (proper part of continuant at all times) - -AnnotationAssertion(obo:BFO_0000179 obo:BFO_0000137 "c-ppart-of_at") -AnnotationAssertion(obo:BFO_0000180 obo:BFO_0000137 "properContinuantPartOfAt") -AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000137 "b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001])"@en) -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000137 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'.") -AnnotationAssertion(obo:IAO_0000412 obo:BFO_0000137 "http://purl.obolibrary.org/obo/bfo.owl") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000137 "(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001] ") -AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000137 obo:bfo.owl) -AnnotationAssertion(rdfs:label obo:BFO_0000137 "proper part of continuant at all times"@en) -SubObjectPropertyOf(obo:BFO_0000137 obo:BFO_0000177) -InverseObjectProperties(obo:BFO_0000137 obo:BFO_0000187) -TransitiveObjectProperty(obo:BFO_0000137) - -# Object Property: obo:BFO_0000177 (part of continuant at all times) - -AnnotationAssertion(obo:BFO_0000179 obo:BFO_0000177 "c-part-of_at") -AnnotationAssertion(obo:BFO_0000180 obo:BFO_0000177 "continuantPartOfAt") -AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000177 "Mary’s arm continuant_part_of Mary in the time of her life prior to her operation"@en) -AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000177 "the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists."@en) -AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000177 "[copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000177 "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000177 "BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])"@en) -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000177 "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion."@en) -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000177 "BFO2 Reference: continuant") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000177 "BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000177 "[copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'") -AnnotationAssertion(obo:IAO_0000412 obo:BFO_0000177 "http://purl.obolibrary.org/obo/bfo.owl") -AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000177 "b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])"@en) -AnnotationAssertion(obo:IAO_0000601 obo:BFO_0000177 "continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])"@en) -AnnotationAssertion(obo:IAO_0000601 obo:BFO_0000177 "continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])"@en) -AnnotationAssertion(obo:IAO_0000601 obo:BFO_0000177 "continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])"@en) -AnnotationAssertion(obo:IAO_0000601 obo:BFO_0000177 "continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])"@en) -AnnotationAssertion(obo:IAO_0000601 obo:BFO_0000177 "continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])"@en) -AnnotationAssertion(obo:IAO_0000601 obo:BFO_0000177 "if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])"@en) -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000177 "(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] ") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000177 "(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] ") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000177 "(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] ") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000177 "(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] ") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000177 "(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] ") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000177 "(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] ") -AnnotationAssertion(obo:IAO_0000602 obo:BFO_0000177 "(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] ") -AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000177 obo:bfo.owl) -AnnotationAssertion(rdfs:label obo:BFO_0000177 "part of continuant at all times"@en) -SubObjectPropertyOf(obo:BFO_0000177 owl:topObjectProperty) -TransitiveObjectProperty(obo:BFO_0000177) -ReflexiveObjectProperty(obo:BFO_0000177) - -# Object Property: obo:BFO_0000187 (has continuant part at all times that part exists) - -AnnotationAssertion(obo:BFO_0000179 obo:BFO_0000187 "c-has-part-object_at") -AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000187 "[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation") -AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000187 "[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.") -AnnotationAssertion(obo:IAO_0000115 obo:BFO_0000187 "forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000187 "This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000187 "[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000187 "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000187 "[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000187 "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant") -AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000187 "[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.") -AnnotationAssertion(obo:IAO_0000412 obo:BFO_0000187 "http://purl.obolibrary.org/obo/bfo.owl") -AnnotationAssertion(obo:IAO_0000600 obo:BFO_0000187 "[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])") -AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000187 obo:bfo.owl) -AnnotationAssertion(rdfs:label obo:BFO_0000187 "has continuant part at all times that part exists"@en) -SubObjectPropertyOf(obo:BFO_0000187 owl:topObjectProperty) - -# Object Property: obo:GEO_000000328 (is in aggregate) - -AnnotationAssertion(rdfs:label obo:GEO_000000328 "is in aggregate"@en) - -# Object Property: obo:GEO_000000329 (is subordinate authority of) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000329 "A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2."@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000329 " -'is subordinate authority of' -Domain: governing organization -Range: governing organization -Formal properties: transitive, anti-symmetric, irreflexive -Natural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2.") -AnnotationAssertion(rdfs:label obo:GEO_000000329 "is subordinate authority of"@en) -IrreflexiveObjectProperty(obo:GEO_000000329) -ObjectPropertyDomain(obo:GEO_000000329 obo:GEO_000000400) -ObjectPropertyRange(obo:GEO_000000329 obo:GEO_000000400) - -# Object Property: obo:GEO_000000336 (has jurisdiction in) - -AnnotationAssertion(rdfs:comment obo:GEO_000000336 "It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c. - -in other words, it is perfectly fine to say: -a disjoint b -c has_jurisdiction_in a -c has_jurisdiction_in b - -otherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it \"United States territory\", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities."@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000336 "a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories."@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000336 "if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000336 "has jurisdiction in"@en) -AsymmetricObjectProperty(obo:GEO_000000336) -IrreflexiveObjectProperty(obo:GEO_000000336) -ObjectPropertyDomain(obo:GEO_000000336 obo:GEO_000000400) -ObjectPropertyRange(obo:GEO_000000336 obo:GEO_000000375) - -# Object Property: obo:IAO_0000039 (has measurement unit label) - -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000039 "has measurement unit label"@en) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000039 "A relation between a value specification and its unit of measurement.") -AnnotationAssertion(obo:IAO_0000412 obo:IAO_0000039 "http://purl.obolibrary.org/obo/obi.owl") -SubObjectPropertyOf(obo:IAO_0000039 obo:BFO_0000051) - -# Object Property: obo:IAO_0000136 (is about) - -AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000136 "This document is about information artifacts and their representations"@en) -AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000136 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000136 "is_about is a (currently) primitive relation that relates an information artifact to an entity."@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000136 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic."@en) -AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000136 "person:Alan Ruttenberg"@en) -AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000136 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) -AnnotationAssertion(obo:IAO_0000412 obo:IAO_0000136 "http://purl.obolibrary.org/obo/iao.owl") -AnnotationAssertion(rdfs:label obo:IAO_0000136 "is about"@en) -SubObjectPropertyOf(obo:IAO_0000136 owl:topObjectProperty) - -# Object Property: obo:OBI_0000293 (has_specified_input) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000293 "has_specified_input"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000293 "see is_input_of example_of_usage"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000293 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000293 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Bjoern Peters") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Larry Hunter") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Melanie Coutot") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000293 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000293 "has_specified_input"@en) -SubObjectPropertyOf(obo:OBI_0000293 obo:RO_0000057) - -# Object Property: obo:OBI_0000295 (is_specified_input_of) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000295 "is_specified_input_of"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000295 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000295 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000295 "Alan Ruttenberg"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000295 "PERSON:Bjoern Peters") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000295 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000295 "is_specified_input_of"@en) -SubObjectPropertyOf(obo:OBI_0000295 obo:RO_0000056) - -# Object Property: obo:OBI_0000299 (has_specified_output) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000299 "has_specified_output"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000299 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Bjoern Peters") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Larry Hunter") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Melanie Courtot") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000299 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000299 "has_specified_output"@en) -SubObjectPropertyOf(obo:OBI_0000299 obo:RO_0000057) - -# Object Property: obo:OBI_0000312 (is_specified_output_of) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000312 "is_specified_output_of"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000312 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000312 "Alan Ruttenberg"@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000312 "PERSON:Bjoern Peters") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000312 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0000312 "is_specified_output_of"@en) -SubObjectPropertyOf(obo:OBI_0000312 obo:RO_0000056) - -# Object Property: obo:OBI_0001938 (has value specification) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001938 "has value specification") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001938 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001938 "A relation between an information content entity and a value specification that specifies its value.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001938 "PERSON: James A. Overton") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001938 "OBI") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001938 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0001938 "has value specification") -SubObjectPropertyOf(obo:OBI_0001938 owl:topObjectProperty) - -# Object Property: obo:RO_0000056 (participates in) - -AnnotationAssertion(obo:IAO_0000111 obo:RO_0000056 "participates in"@en) -AnnotationAssertion(obo:IAO_0000118 obo:RO_0000056 "participates_in"@en) -AnnotationAssertion(obo:IAO_0000412 obo:RO_0000056 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:RO_0000056 "participates in"@en) -SubObjectPropertyOf(obo:RO_0000056 owl:topObjectProperty) - -# Object Property: obo:RO_0000057 (has participant) - -AnnotationAssertion(obo:IAO_0000111 obo:RO_0000057 "has participant"@en) -AnnotationAssertion(obo:IAO_0000118 obo:RO_0000057 "has_participant"@en) -AnnotationAssertion(obo:IAO_0000412 obo:RO_0000057 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:RO_0000057 "has participant"@en) -SubObjectPropertyOf(obo:RO_0000057 owl:topObjectProperty) - - -############################ -# Data Properties -############################ - -# Data Property: obo:IAO_0000004 (has measurement value) - -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000004 "A relation between a scalar measurement data item and a number that quantifies it.") -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000004 "The range should probably not be restricted to \"float\". It makes sense to set it to \"real\". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now.") -AnnotationAssertion(obo:IAO_0000412 obo:IAO_0000004 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:IAO_0000004 "has measurement value"@en) -FunctionalDataProperty(obo:IAO_0000004) -DataPropertyDomain(obo:IAO_0000004 obo:IAO_0000032) -DataPropertyRange(obo:IAO_0000004 xsd:double) - ############################ # Classes ############################ -# Class: obo:GEO_000000001 (geopolitical entity) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000001 "An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii)"@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000001 "William R. Hogan"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000001 "In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000001 "geopolitical entity"@en) -AnnotationAssertion(owl:deprecated obo:GEO_000000001 "true"^^xsd:boolean) -SubClassOf(obo:GEO_000000001 oboInOwl:ObsoleteClass) - -# Class: obo:GEO_000000002 (obsolete group of governmental organizations) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000000002 "obsolete aggregate of governmental organizations"@en) -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000002 "An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on."@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000002 "William R. Hogan"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000002 "taken over by GEO_0000000401"@en) -AnnotationAssertion(rdfs:label obo:GEO_000000002 "obsolete group of governmental organizations"@en) -AnnotationAssertion(owl:deprecated obo:GEO_000000002 "true"^^xsd:boolean) -EquivalentClasses(obo:GEO_000000002 ObjectSomeValuesFrom(obo:BFO_0000075 ObjectUnionOf(obo:GEO_000000391 obo:GEO_000000400))) -SubClassOf(obo:GEO_000000002 obo:BFO_0000004) - -# Class: obo:GEO_000000003 (nation) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000003 "A geopolitical entity that is self contained and recognizes no higher political authority than itself."@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000003 "William R. Hogan"@en) -AnnotationAssertion(rdfs:label obo:GEO_000000003 "nation"@en) -AnnotationAssertion(owl:deprecated obo:GEO_000000003 "true"^^xsd:boolean) -SubClassOf(obo:GEO_000000003 oboInOwl:ObsoleteClass) - # Class: obo:GEO_000000004 (subnational entity) AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000004 "a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority"@en) AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000004 "Amanda Hicks"@en) AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000004 "William R. Hogan"@en) AnnotationAssertion(rdfs:label obo:GEO_000000004 "subnational entity"@en) -EquivalentClasses(obo:GEO_000000004 ObjectIntersectionOf(obo:GEO_000000400 ObjectSomeValuesFrom(obo:GEO_000000329 obo:GEO_000000396))) SubClassOf(obo:GEO_000000004 obo:GEO_000000400) # Class: obo:GEO_000000005 (major administrative subdivision) @@ -662,66 +72,6 @@ AnnotationAssertion(rdfs:comment obo:GEO_000000006 "Typically, the common featur AnnotationAssertion(rdfs:label obo:GEO_000000006 "geopolitical dependency"@en) SubClassOf(obo:GEO_000000006 obo:GEO_000000004) -# Class: obo:GEO_000000007 (aggregate of major administrative subdivisions) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000007 "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common."@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000007 "Amanda Hicks"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000007 "Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000007 "aggregate of major administrative subdivisions"@en) -AnnotationAssertion(rdfs:label obo:GEO_000000007 "group of major administrative subdivisions"@en) -EquivalentClasses(obo:GEO_000000007 ObjectIntersectionOf(ObjectComplementOf(obo:GEO_000000005) ObjectAllValuesFrom(obo:BFO_0000075 obo:GEO_000000005) ObjectMinCardinality(2 obo:BFO_0000075 obo:GEO_000000005))) -SubClassOf(obo:GEO_000000007 obo:GEO_000000337) - -# Class: obo:GEO_000000008 (group of dependencies) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000008 "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common."@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000008 "Amanda Hicks"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000008 "Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000008 "aggregate of dependencies"@en) -AnnotationAssertion(rdfs:label obo:GEO_000000008 "group of dependencies"@en) -EquivalentClasses(obo:GEO_000000008 ObjectIntersectionOf(ObjectComplementOf(obo:GEO_000000006) ObjectAllValuesFrom(obo:BFO_0000075 obo:GEO_000000006) ObjectMinCardinality(2 obo:BFO_0000075 obo:GEO_000000006))) -SubClassOf(obo:GEO_000000008 obo:GEO_000000337) - -# Class: obo:GEO_000000334 (subcontinental land mass) - -AnnotationAssertion(rdfs:label obo:GEO_000000334 "subcontinental land mass"@en) -SubClassOf(obo:GEO_000000334 obo:GEO_000000375) -SubClassOf(obo:GEO_000000334 ObjectSomeValuesFrom(obo:BFO_0000137 obo:GEO_000000374)) - -# Class: obo:GEO_000000335 (contiguous land mass) - -AnnotationAssertion(obo:IAO_0000118 obo:GEO_000000335 "contiguous continental land mass"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000335 "per the definition of 'contiguous' of \"being in actual contact : touching along a boundary or at a point\", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island. - -At some point, we need an 'adjacent to' relation if BFO doesn't provide it. - -One question is whether this class encompasses fiat parts of islands."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000335 "contiguous land mass"@en) -SubClassOf(obo:GEO_000000335 obo:GEO_000000334) - -# Class: obo:GEO_000000337 (aggregate of governmental organizations) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000337 "An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members. -"@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000337 "William R. Hogan") -AnnotationAssertion(rdfs:label obo:GEO_000000337 "aggregate of governmental organizations"@en) -EquivalentClasses(obo:GEO_000000337 ObjectIntersectionOf(ObjectComplementOf(obo:GEO_000000400) ObjectAllValuesFrom(obo:BFO_0000075 obo:GEO_000000400) ObjectMinCardinality(2 obo:BFO_0000075 obo:GEO_000000400))) -SubClassOf(obo:GEO_000000337 obo:BFO_0000004) - -# Class: obo:GEO_000000357 (contiguous island land mass) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000357 "A subcontinental land mass that is part of an island and includes part of the land surface of the island."@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000357 "William R. Hogan") -AnnotationAssertion(rdfs:comment obo:GEO_000000357 "It cannot be a part of the island, for example, that is below water."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000357 "contiguous island land mass"@en) -SubClassOf(obo:GEO_000000357 obo:GEO_000000334) - -# Class: obo:GEO_000000369 (aggregate of contiguous land masses) - -AnnotationAssertion(rdfs:label obo:GEO_000000369 "aggregate of contiguous land masses"@en) -EquivalentClasses(obo:GEO_000000369 ObjectSomeValuesFrom(obo:BFO_0000075 obo:GEO_000000375)) -SubClassOf(obo:GEO_000000369 obo:GEO_000000375) - # Class: obo:GEO_000000370 (geographical entity) AnnotationAssertion(obo:IAO_0000111 obo:GEO_000000370 "geographical entity of astronomical body"@en) @@ -756,45 +106,6 @@ AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000372 "William R. Hogan"@en) AnnotationAssertion(rdfs:label obo:GEO_000000372 "geographical region"@en) SubClassOf(obo:GEO_000000372 obo:GEO_000000370) -# Class: obo:GEO_000000373 (body of water) - -AnnotationAssertion(rdfs:label obo:GEO_000000373 "body of water"@en) -SubClassOf(obo:GEO_000000373 obo:GEO_000000372) - -# Class: obo:GEO_000000374 (continent) - -AnnotationAssertion(rdfs:label obo:GEO_000000374 "continent"@en) -SubClassOf(obo:GEO_000000374 obo:GEO_000000375) - -# Class: obo:GEO_000000375 (land mass) - -AnnotationAssertion(rdfs:label obo:GEO_000000375 "land mass"@en) -SubClassOf(obo:GEO_000000375 obo:GEO_000000372) - -# Class: obo:GEO_000000376 (island) - -AnnotationAssertion(rdfs:label obo:GEO_000000376 "island"@en) -SubClassOf(obo:GEO_000000376 obo:GEO_000000334) - -# Class: obo:GEO_000000377 (aggregate of geographical entities) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000377 "An object aggregate of geographical entities"@en) -AnnotationAssertion(rdfs:label obo:GEO_000000377 "aggregate of geographical entities"@en) -EquivalentClasses(obo:GEO_000000377 ObjectSomeValuesFrom(obo:BFO_0000075 obo:GEO_000000370)) -SubClassOf(obo:GEO_000000377 obo:BFO_0000027) - -# Class: obo:GEO_000000378 (aggregate of geographical features) - -AnnotationAssertion(rdfs:label obo:GEO_000000378 "aggregate of geographical features"@en) -EquivalentClasses(obo:GEO_000000378 ObjectSomeValuesFrom(obo:BFO_0000075 obo:GEO_000000371)) -SubClassOf(obo:GEO_000000378 obo:GEO_000000377) - -# Class: obo:GEO_000000390 (aggregate of islands) - -AnnotationAssertion(rdfs:label obo:GEO_000000390 "aggregate of islands"@en) -EquivalentClasses(obo:GEO_000000390 ObjectSomeValuesFrom(obo:BFO_0000075 obo:GEO_000000376)) -SubClassOf(obo:GEO_000000390 obo:GEO_000000369) - # Class: obo:GEO_000000391 (geopoli organization) AnnotationAssertion(obo:IAO_0000111 obo:GEO_000000391 "geopolitical organization"@en) @@ -859,58 +170,6 @@ AnnotationAssertion(rdfs:comment obo:GEO_000000400 "IMPORTANT: The label \"geopo AnnotationAssertion(rdfs:label obo:GEO_000000400 "governmental organization"@en) SubClassOf(obo:GEO_000000400 obo:OBI_0000245) -# Class: obo:GEO_000000401 (aggregate of geopolitical organizations) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000401 "An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common"@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000401 "Amanda Hicks"@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000401 "William R. Hogan -"@en) -AnnotationAssertion(obo:IAO_0000412 obo:GEO_000000401 "http://purl.obolibrary.org/obo/omrse.owl") -AnnotationAssertion(rdfs:label obo:GEO_000000401 "aggregate of geopolitical organizations"@en) -EquivalentClasses(obo:GEO_000000401 ObjectIntersectionOf(ObjectComplementOf(obo:GEO_000000391) ObjectAllValuesFrom(obo:BFO_0000075 obo:GEO_000000391) ObjectMinCardinality(2 obo:BFO_0000075 obo:GEO_000000391))) -SubClassOf(obo:GEO_000000401 obo:BFO_0000004) - -# Class: obo:GEO_000000402 (obsolete aggregate of dependencies) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000402 "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common."@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000402 "Amanda Hicks"@en) -AnnotationAssertion(obo:IAO_0000412 obo:GEO_000000402 "http://purl.obolibrary.org/obo/omrse.owl") -AnnotationAssertion(rdfs:comment obo:GEO_000000402 "Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000402 "obsolete aggregate of dependencies"@en) -AnnotationAssertion(owl:deprecated obo:GEO_000000402 "true"^^xsd:boolean) -SubClassOf(obo:GEO_000000402 obo:GEO_000000337) - -# Class: obo:GEO_000000403 (obsolete aggregate of major administrative subdivisions) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000403 "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common"@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000403 "Amanda Hicks"@en) -AnnotationAssertion(obo:IAO_0000412 obo:GEO_000000403 "http://purl.obolibrary.org/obo/omrse.owl") -AnnotationAssertion(rdfs:comment obo:GEO_000000403 "Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000403 "obsolete aggregate of major administrative subdivisions"@en) -AnnotationAssertion(owl:deprecated obo:GEO_000000403 "true"^^xsd:boolean) -SubClassOf(obo:GEO_000000403 obo:GEO_000000337) - -# Class: obo:GEO_000000404 (aggregate of sovereign states) - -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000404 "An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common"@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000404 "William R. Hogan"@en) -AnnotationAssertion(obo:IAO_0000412 obo:GEO_000000404 "http://purl.obolibrary.org/obo/omrse.owl") -AnnotationAssertion(rdfs:comment obo:GEO_000000404 "examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000404 "aggregate of sovereign states"@en) -EquivalentClasses(obo:GEO_000000404 ObjectIntersectionOf(ObjectComplementOf(obo:GEO_000000396) ObjectAllValuesFrom(obo:BFO_0000075 obo:GEO_000000396) ObjectMinCardinality(2 obo:BFO_0000075 obo:GEO_000000396))) -SubClassOf(obo:GEO_000000404 obo:GEO_000000337) - -# Class: obo:GEO_000000787 (geodetic coordinate measurement datum) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000000787 "geodetic coordinate measurement datum"@en) -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000787 "A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum."@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000787 "Josh Hanna"@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000787 "William R. Hogan"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000787 "latitude and longitude are key subtypes"@en) -AnnotationAssertion(rdfs:label obo:GEO_000000787 "geodetic coordinate measurement datum"@en) -EquivalentClasses(obo:GEO_000000787 ObjectIntersectionOf(obo:IAO_0000109 ObjectSomeValuesFrom(obo:OBI_0000312 ObjectIntersectionOf(obo:BFO_0000015 ObjectSomeValuesFrom(obo:OBI_0000293 obo:GEO_000000788))) ObjectSomeValuesFrom(obo:OBI_0001938 ObjectIntersectionOf(obo:OBI_0001933 ObjectHasValue(obo:IAO_0000039 obo:GEO_000000790))))) -SubClassOf(obo:GEO_000000787 obo:IAO_0000109) - # Class: obo:GEO_000000788 (geodetic datum) AnnotationAssertion(obo:IAO_0000111 obo:GEO_000000788 "geodetic datum"@en) @@ -924,12 +183,6 @@ AnnotationAssertion(rdfs:comment obo:GEO_000000788 "Every latitude and longitude AnnotationAssertion(rdfs:label obo:GEO_000000788 "geodetic datum"@en) SubClassOf(obo:GEO_000000788 obo:IAO_0000030) -# Class: obo:GEO_000000789 (plane angle measurement unit label) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000000789 "planar angular measurement unit label"@en) -AnnotationAssertion(rdfs:label obo:GEO_000000789 "plane angle measurement unit label"@en) -SubClassOf(obo:GEO_000000789 obo:IAO_0000003) - # Class: obo:GEO_000000797 (de jure sovereign state) AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000797 "A sovereign state whose political sovereignty has been recognized by the United Nations, in accordance with international law."@en) @@ -939,238 +192,6 @@ AnnotationAssertion(rdfs:comment obo:GEO_000000797 "Sovereignty, in the legal se AnnotationAssertion(rdfs:label obo:GEO_000000797 "de jure sovereign state"@en) SubClassOf(obo:GEO_000000797 obo:GEO_000000396) -# Class: obo:IAO_0000003 (measurement unit label) - -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000003 "measurement unit label"@en) -AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000003 "Examples of measurement unit labels are liters, inches, weight per volume."@en) -AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000003 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000003 "A data item label that denotes a unit of measure."@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000003 "2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term."@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000003 "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI."@en) -AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000003 "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000003 "PERSON: Melanie Courtot"@en) -AnnotationAssertion(obo:IAO_0000412 obo:IAO_0000003 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:IAO_0000003 "measurement unit label"@en) -SubClassOf(obo:IAO_0000003 obo:IAO_0000009) - -# Class: obo:IAO_0000009 (datum label) - -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000009 "data item label"@en) -AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000009 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000009 "An information content entity that is part of some data item and is used to partially define the denotation of that data item."@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000009 "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n"@en) -AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000009 "GROUP: IAO"@en) -AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000009 "datum label") -AnnotationAssertion(obo:IAO_0000232 obo:IAO_0000009 "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. -") -AnnotationAssertion(obo:IAO_0000412 obo:IAO_0000009 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:IAO_0000009 "data item label"@en) -SubClassOf(obo:IAO_0000009 obo:IAO_0000030) - -# Class: obo:IAO_0000032 (scalar measurement datum) - -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000032 "scalar measurement datum"@en) -AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000032 "10 feet. 3 ml."@en) -AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000032 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000032 "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label."@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000032 "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form"@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000032 "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them."@en) -AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000032 "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000032 "PERSON: Melanie Courtot"@en) -AnnotationAssertion(obo:IAO_0000412 obo:IAO_0000032 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:IAO_0000032 "scalar measurement datum"@en) -SubClassOf(obo:IAO_0000032 obo:IAO_0000109) - -# Class: obo:IAO_0000109 (measurement datum) - -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000109 "measurement datum"@en) -AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000109 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}."@en) -AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000109 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000109 "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device."@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000109 "2/2/2009 is_specified_output of some assay?"@en) -AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000109 "person:Chris Stoeckert"@en) -AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000109 "OBI_0000305"@en) -AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000109 "group:OBI"@en) -AnnotationAssertion(obo:IAO_0000412 obo:IAO_0000109 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:IAO_0000109 "measurement datum"@en) -SubClassOf(obo:IAO_0000109 obo:IAO_0000027) - -# Class: obo:OBI_0000245 (organization) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000245 "organization"@en) -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000245 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods."@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000245 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000245 "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en) -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000245 "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: - -1) there are organization_member_roles (president, treasurer, branch -editor), with individual persons as bearers - -2) there are organization_roles (employer, owner, vendor, patent holder) - -3) an organization has a charter / rules / bylaws, which specify what roles -there are, how they should be realized, and how to modify the -charter/rules/bylaws themselves. - -It is debatable what the organization itself is (some kind of dependent -continuant or an aggregate of people). This also determines who/what the -bearer of organization_roles' are. My personal favorite is still to define -organization as a kind of 'legal entity', but thinking it through leads to -all kinds of questions that are clearly outside the scope of OBI. - -Interestingly enough, it does not seem to matter much where we place -organization itself, as long as we can subclass it (University, Corporation, -Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, -W3C, University of Oklahoma), and have it play roles. - -This leads to my proposal: We define organization through the statements 1 - -3 above, but without an 'is a' statement for now. We can leave it in its -current place in the is_a hierarchy (material entity) or move it up to -'continuant'. We leave further clarifications to BFO, and close this issue -for now."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Alan Ruttenberg") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Bjoern Peters") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Philippe Rocca-Serra") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Susanna Sansone") -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000245 "GROUP: OBI") -AnnotationAssertion(rdfs:label obo:OBI_0000245 "organization"@en) -SubClassOf(obo:OBI_0000245 obo:BFO_0000004) - -# Class: obo:OBI_0001620 (latitude coordinate measurement datum) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001620 "latitude coordinate measurement datum"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001620 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001620 "A measurement datum that is the measure of the latitude coordinate of a site."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001620 "Person: Chris Stoeckert, Jie Zheng"@en) -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0001620 "latitude"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001620 "NIAID GSCID-BRC metadata working group"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001620 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(obo:OBI_0001886 obo:OBI_0001620 "Specimen Collection Location - Latitude") -AnnotationAssertion(dc:source obo:OBI_0001620 "NIAID GSCID-BRC") -AnnotationAssertion(rdfs:label obo:OBI_0001620 "latitude coordinate measurement datum"@en) -SubClassOf(obo:OBI_0001620 obo:GEO_000000787) - -# Class: obo:OBI_0001621 (longitude coordinate measurement datum) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001621 "longitude coordinate measurement datum"@en) -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001621 obo:IAO_0000120) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001621 "A measurement datum that is the measure of the longitude coordinate of a site."@en) -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001621 "Person: Chris Stoeckert, Jie Zheng"@en) -AnnotationAssertion(obo:IAO_0000118 obo:OBI_0001621 "longitude"@en) -AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001621 "NIAID GSCID-BRC metadata working group"@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001621 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(obo:OBI_0001886 obo:OBI_0001621 "Specimen Collection Location - Longitude") -AnnotationAssertion(dc:source obo:OBI_0001621 "NIAID GSCID-BRC") -AnnotationAssertion(rdfs:label obo:OBI_0001621 "longitude coordinate measurement datum"@en) -SubClassOf(obo:OBI_0001621 obo:GEO_000000787) - -# Class: obo:OBI_0001931 (scalar value specification) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001931 "scalar value specification") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001931 obo:IAO_0000123) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001931 "A value specification that consists of two parts: a numeral and a unit label") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001931 "PERSON:Bjoern Peters") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001931 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0001931 "scalar value specification") -SubClassOf(obo:OBI_0001931 obo:OBI_0001933) - -# Class: obo:OBI_0001933 (value specification) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001933 "value specification") -AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001933 "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass.") -AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001933 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001933 "An information content entity that specifies a value within a classification scheme or on a quantitative scale.") -AnnotationAssertion(obo:IAO_0000116 obo:OBI_0001933 "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.") -AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001933 "PERSON:Bjoern Peters") -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0001933 "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label obo:OBI_0001933 "value specification") -SubClassOf(obo:OBI_0001933 obo:IAO_0000030) - -# Class: obo:PATO_0000117 (size) - -AnnotationAssertion(obo:IAO_0000115 obo:PATO_0000117 "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.") -AnnotationAssertion(obo:IAO_0000412 obo:PATO_0000117 "http://purl.obolibrary.org/obo/pato.owl") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:PATO_0000117 "quality") -AnnotationAssertion(oboInOwl:id obo:PATO_0000117 "PATO:0000117") -AnnotationAssertion(oboInOwl:inSubset obo:PATO_0000117 ) -AnnotationAssertion(oboInOwl:inSubset obo:PATO_0000117 ) -AnnotationAssertion(rdfs:label obo:PATO_0000117 "size") -SubClassOf(obo:PATO_0000117 obo:PATO_0001241) - -# Class: obo:PATO_0001241 (physical object quality) - -AnnotationAssertion(obo:IAO_0000115 obo:PATO_0001241 "A quality which inheres in a continuant.") -AnnotationAssertion(obo:IAO_0000412 obo:PATO_0001241 "http://purl.obolibrary.org/obo/pato.owl") -AnnotationAssertion(oboInOwl:hasAlternativeId obo:PATO_0001241 "PATO:0001237") -AnnotationAssertion(oboInOwl:hasAlternativeId obo:PATO_0001241 "PATO:0001238") -AnnotationAssertion(oboInOwl:hasDbXref obo:PATO_0001241 "snap:Quality") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:PATO_0001241 "monadic quality of a continuant") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:PATO_0001241 "multiply inhering quality of a physical entity ") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:PATO_0001241 "quality of a continuant") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:PATO_0001241 "quality of a single physical entity") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:PATO_0001241 "quality of an object") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:PATO_0001241 "quality of continuant") -AnnotationAssertion(oboInOwl:hasNarrowSynonym obo:PATO_0001241 "monadic quality of an object") -AnnotationAssertion(oboInOwl:hasNarrowSynonym obo:PATO_0001241 "monadic quality of continuant") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:PATO_0001241 "quality") -AnnotationAssertion(oboInOwl:id obo:PATO_0001241 "PATO:0001241") -AnnotationAssertion(rdfs:comment obo:PATO_0001241 "Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.") -AnnotationAssertion(rdfs:label obo:PATO_0001241 "physical object quality") -SubClassOf(obo:PATO_0001241 obo:BFO_0000019) - -# Class: obo:PATO_0001323 (area) - -AnnotationAssertion(obo:IAO_0000115 obo:PATO_0001323 "A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent.") -AnnotationAssertion(obo:IAO_0000412 obo:PATO_0001323 "http://purl.obolibrary.org/obo/pato.owl") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:PATO_0001323 "quality") -AnnotationAssertion(oboInOwl:id obo:PATO_0001323 "PATO:0001323") -AnnotationAssertion(oboInOwl:inSubset obo:PATO_0001323 ) -AnnotationAssertion(oboInOwl:inSubset obo:PATO_0001323 ) -AnnotationAssertion(oboInOwl:inSubset obo:PATO_0001323 ) -AnnotationAssertion(rdfs:comment obo:PATO_0001323 "MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area."@en) -AnnotationAssertion(rdfs:label obo:PATO_0001323 "area") -SubClassOf(obo:PATO_0001323 obo:PATO_0001709) - -# Class: obo:PATO_0001709 (2-D extent) - -AnnotationAssertion(obo:IAO_0000115 obo:PATO_0001709 "A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions.") -AnnotationAssertion(obo:IAO_0000412 obo:PATO_0001709 "http://purl.obolibrary.org/obo/pato.owl") -AnnotationAssertion(oboInOwl:hasExactSynonym obo:PATO_0001709 "2-D size") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:PATO_0001709 "quality") -AnnotationAssertion(oboInOwl:id obo:PATO_0001709 "PATO:0001709") -AnnotationAssertion(oboInOwl:inSubset obo:PATO_0001709 ) -AnnotationAssertion(rdfs:label obo:PATO_0001709 "2-D extent") -SubClassOf(obo:PATO_0001709 obo:PATO_0000117) - -# Class: obo:UO_0000047 (area unit) - -AnnotationAssertion(obo:IAO_0000115 obo:UO_0000047 "A unit which is a standard measure of the amount of a 2-dimensional flat surface.") -AnnotationAssertion(obo:IAO_0000412 obo:UO_0000047 "http://purl.obolibrary.org/obo/uo.owl") -AnnotationAssertion(oboInOwl:created_by obo:UO_0000047 "george gkoutos") -AnnotationAssertion(oboInOwl:hasOBONamespace obo:UO_0000047 "unit.ontology") -AnnotationAssertion(oboInOwl:id obo:UO_0000047 "UO:0000047") -AnnotationAssertion(oboInOwl:inSubset obo:UO_0000047 ) -AnnotationAssertion(rdfs:label obo:UO_0000047 "area unit") -SubClassOf(obo:UO_0000047 obo:IAO_0000003) - -# Class: (supranational entity) - -AnnotationAssertion(obo:IAO_0000117 "Amanda Hicks"@en) -AnnotationAssertion(rdfs:comment "e.g., the EU") -AnnotationAssertion(rdfs:label "supranational entity"@en) -SubClassOf( obo:GEO_000000400) - -# Class: oboInOwl:ObsoleteClass (obsolete_class) - -AnnotationAssertion(obo:IAO_0000412 oboInOwl:ObsoleteClass "http://www.geneontology.org/formats/oboInOwl") -AnnotationAssertion(oboInOwl:hasDefinition oboInOwl:ObsoleteClass _:genid2147484129) -AnnotationAssertion(rdfs:label oboInOwl:ObsoleteClass "obsolete_class"@en) - ############################ # Named Individuals @@ -1181,32 +202,6 @@ AnnotationAssertion(rdfs:label oboInOwl:ObsoleteClass "obsolete_class"@en) AnnotationAssertion(obo:IAO_0000111 obo:GEO_000000790 "angular degree"@en) AnnotationAssertion(rdfs:label obo:GEO_000000790 "angular degree"@en) AnnotationAssertion(rdfs:label obo:GEO_000000790 "°"@en) -ClassAssertion(obo:GEO_000000789 obo:GEO_000000790) - -# Individual: obo:GEO_000000791 (rad) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000000791 "radian"@en) -AnnotationAssertion(obo:IAO_0000115 obo:GEO_000000791 "A unit of measurement of planar angles where a full circle is 2π. Specifically the angle is the length of the arc subtended by the angle divided by the circumference of the circle."@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000791 "Josh Hanna"@en) -AnnotationAssertion(obo:IAO_0000117 obo:GEO_000000791 "William R. Hogan"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000791 "Technically in the S.I. system it is a derived unit m•m^-1."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000791 "rad"@en) -AnnotationAssertion(rdfs:label obo:GEO_000000791 "radian"@en) -ClassAssertion(obo:GEO_000000789 obo:GEO_000000791) - -# Individual: obo:GEO_000000796 (square mile) - -AnnotationAssertion(obo:IAO_0000111 obo:GEO_000000796 "square mile"@en) -AnnotationAssertion(rdfs:comment obo:GEO_000000796 "An area unit which is equal to the area enclosed by a square in a flat plane which is one mile on every side."@en) -AnnotationAssertion(rdfs:label obo:GEO_000000796 "square mile"@en) -ClassAssertion(obo:UO_0000047 obo:GEO_000000796) - -# Individual: obo:UO_0000080 (square meter) - -AnnotationAssertion(rdfs:comment obo:UO_0000080 "\"An area unit which is equal to an area enclosed by a square with sides each 1 meter long.\" [NIST:NIST]") -AnnotationAssertion(rdfs:label obo:UO_0000080 "square meter") -ClassAssertion(obo:UO_0000047 obo:UO_0000080) -AnnotationAssertion(rdfs:label obo:BFO_0000050 "part_of"@en) ) \ No newline at end of file diff --git a/src/ontology/imports/geo_terms.txt b/src/ontology/imports/geo_terms.txt index 139597f..b2e19f4 100644 --- a/src/ontology/imports/geo_terms.txt +++ b/src/ontology/imports/geo_terms.txt @@ -1,2 +1,18 @@ - - +GEO:000000005 +GEO:000000372 +GEO:000000371 +GEO:000000370 +GEO:000000790 +GEO:000000788 +GEO:000000391 +GEO:000000400 +GEO:000000396 +GEO:000000004 +GEO:000000399 +GEO:000000006 +GEO:000000797 +GEO:000000395 +GEO:000000393 +GEO:000000392 +OBI:0001933 +OBI:0001931 diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index 1997ccb..4fb44f9 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2026-03-13") + +Annotation( ) +Annotation(owl:versionInfo "2026-07-19") Declaration(Class()) Declaration(Class()) @@ -35,6 +35,7 @@ Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -77,6 +78,14 @@ Declaration(AnnotationProperty(rdfs:label)) AnnotationAssertion(rdfs:label "definition") +# Annotation Property: (term tracker item) + +AnnotationAssertion( "IAO:0000233") +AnnotationAssertion( "external") +AnnotationAssertion( "term_tracker_item") +AnnotationAssertion( "term_tracker_item") +AnnotationAssertion(rdfs:label "term tracker item") + # Annotation Property: (term replaced by) AnnotationAssertion(rdfs:label "term replaced by") @@ -288,6 +297,7 @@ SubClassOf( (biological_process) AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24968"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:05:24Z") AnnotationAssertion( "GO:0000004") @@ -348,6 +358,7 @@ SubClassOf( (reproductive behavior) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:pr") "The specific behavior of an organism that is associated with reproduction.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23491"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T16:01:37Z") AnnotationAssertion( "GO:0033057") @@ -368,6 +379,7 @@ SubClassOf( (sexual reproduction) AnnotationAssertion(Annotation( "Wikipedia:Sexual_reproduction") "A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22929"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Sexual_reproduction") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0019953") @@ -379,6 +391,7 @@ SubClassOf( (asexual reproduction) AnnotationAssertion(Annotation( "ISBN:0387520546") Annotation( "PMID:22977071") Annotation( "PMID:28779329") Annotation( "PMID:29559496") "A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22929"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Asexual_reproduction") AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "Wikipedia:Parthenogenesis") "parthenogenesis") @@ -389,6 +402,7 @@ SubClassOf( (reproductive process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:isa_complete") "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T15:56:06Z") AnnotationAssertion( "GO:0019952") @@ -412,6 +426,7 @@ SubClassOf( (multicellular organismal process) AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T16:07:47Z") AnnotationAssertion( "GO:0044707") @@ -429,10 +444,13 @@ SubClassOf( (biological process involved in symbiotic interaction) AnnotationAssertion(Annotation( "GOC:cc") Annotation( "PMID:31257129") "A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14807"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20191"^^xsd:anyURI) AnnotationAssertion( "GO:0043298") AnnotationAssertion( "GO:0044404") AnnotationAssertion( "GO:0072519") AnnotationAssertion( "GO:0085031") +AnnotationAssertion(Annotation(rdfs:label "Dengue Virus Infection") "Reactome:R-HSA-9839923") AnnotationAssertion( "commensalism") AnnotationAssertion( "host-pathogen interaction") AnnotationAssertion( "parasitism") @@ -452,6 +470,7 @@ SubClassOf( (symbiont entry into host) AnnotationAssertion(Annotation( "GOC:vw") "Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18563"^^xsd:anyURI) AnnotationAssertion( "GO:0030260") AnnotationAssertion( "GO:0044411") AnnotationAssertion( "GO:0051806") @@ -491,6 +510,7 @@ SubClassOf( (biological process involved in interspecies interaction between organisms) AnnotationAssertion(Annotation( "GOC:cc") "Any process evolved to enable an interaction with an organism of a different species.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20191"^^xsd:anyURI) AnnotationAssertion(Annotation(rdfs:label "Parasitic Infection Pathways") "Reactome:R-HSA-9824443") AnnotationAssertion( "interaction with another species") AnnotationAssertion( "interspecies interaction") @@ -507,6 +527,7 @@ SubClassOf( (multicellular organismal reproductive process) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") Annotation( "GOC:tb") "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) AnnotationAssertion( "organismal reproductive process") AnnotationAssertion(Annotation(rdfs:label "Reproduction") "Reactome:R-HSA-1474165") AnnotationAssertion( "reproductive process in a multicellular organism") @@ -520,6 +541,7 @@ SubClassOf( (biological process involved in interaction with host) AnnotationAssertion(Annotation( "GOC:cc") "An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20191"^^xsd:anyURI) AnnotationAssertion( "GO:0044112") AnnotationAssertion( "GO:0044116") AnnotationAssertion( "GO:0044117") @@ -528,6 +550,7 @@ AnnotationAssertion( "GO:0044123") AnnotationAssertion( "GO:0044125") AnnotationAssertion(Annotation(rdfs:label "Infection with Mycobacterium tuberculosis") "Reactome:R-HSA-9635486") +AnnotationAssertion(Annotation(rdfs:label "Infection with Enterobacteria") "Reactome:R-HSA-9640148") AnnotationAssertion(Annotation(rdfs:label "Leishmania infection") "Reactome:R-HSA-9658195") AnnotationAssertion( "interaction with host") AnnotationAssertion( "growth of symbiont in host") diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 0096e00..d9c0625 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -5,6 +5,7 @@ Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) +Prefix(xsp:=) Prefix(foaf:=) Prefix(rdfs:=) Prefix(swrl:=) @@ -15,9 +16,9 @@ Prefix(oboInOwl:=) Ontology( - -Annotation(dc:source ) -Annotation(owl:versionInfo "2026-03-13") + +Annotation(dc:source ) +Annotation(owl:versionInfo "2026-07-19") Declaration(Class(obo:APOLLO_SV_00000008)) Declaration(Class(obo:APOLLO_SV_00000032)) @@ -60,6 +61,8 @@ Declaration(Class(obo:BFO_0000146)) Declaration(Class(obo:BFO_0000147)) Declaration(Class(obo:BFO_0000148)) Declaration(Class(obo:BFO_0000182)) +Declaration(Class(obo:COB_0000035)) +Declaration(Class(obo:COB_0000082)) Declaration(Class(obo:IAO_0000001)) Declaration(Class(obo:IAO_0000003)) Declaration(Class(obo:IAO_0000005)) @@ -232,6 +235,7 @@ Declaration(Class(obo:IAO_0000646)) Declaration(Class(obo:IAO_0000647)) Declaration(Class(obo:IAO_0000648)) Declaration(Class(obo:IAO_0000650)) +Declaration(Class(obo:IAO_0000651)) Declaration(Class(obo:IAO_0000701)) Declaration(Class(obo:IAO_0000702)) Declaration(Class(obo:IAO_0000703)) @@ -240,6 +244,7 @@ Declaration(Class(obo:IAO_0000705)) Declaration(Class(obo:IAO_0000706)) Declaration(Class(obo:IAO_0000707)) Declaration(Class(obo:IAO_0000708)) +Declaration(Class(obo:IAO_0001000)) Declaration(Class(obo:IAO_0020000)) Declaration(Class(obo:IAO_0020001)) Declaration(Class(obo:IAO_0020010)) @@ -268,7 +273,6 @@ Declaration(Class(obo:IAO_8000017)) Declaration(Class(obo:IAO_8000018)) Declaration(Class(obo:IAO_8000019)) Declaration(Class(obo:IAO_8000020)) -Declaration(Class(obo:OBI_0000011)) Declaration(Class(obo:OBI_0000066)) Declaration(Class(obo:OBI_0000471)) Declaration(Class(obo:OBI_0200000)) @@ -288,6 +292,7 @@ Declaration(ObjectProperty(obo:BFO_0000054)) Declaration(ObjectProperty(obo:BFO_0000055)) Declaration(ObjectProperty(obo:BFO_0000066)) Declaration(ObjectProperty(obo:BFO_0000067)) +Declaration(ObjectProperty(obo:IAO_0000011)) Declaration(ObjectProperty(obo:IAO_0000039)) Declaration(ObjectProperty(obo:IAO_0000135)) Declaration(ObjectProperty(obo:IAO_0000136)) @@ -359,6 +364,7 @@ Declaration(NamedIndividual(obo:IAO_0000421)) Declaration(NamedIndividual(obo:IAO_0000423)) Declaration(NamedIndividual(obo:IAO_0000428)) Declaration(NamedIndividual(obo:OMO_0001000)) +Declaration(NamedIndividual(obo:OMO_0001002)) Declaration(AnnotationProperty(protege:defaultLanguage)) Declaration(AnnotationProperty(obo:BFO_0000179)) Declaration(AnnotationProperty(obo:BFO_0000180)) @@ -398,6 +404,22 @@ Declaration(AnnotationProperty(obo:IAO_0010000)) Declaration(AnnotationProperty(obo:IAO_0100001)) Declaration(AnnotationProperty(obo:OMO_0001001)) Declaration(AnnotationProperty(obo:OMO_0002000)) +Declaration(AnnotationProperty(obo:OMO_0002001)) +Declaration(AnnotationProperty(obo:OMO_0003000)) +Declaration(AnnotationProperty(obo:OMO_0003001)) +Declaration(AnnotationProperty(obo:OMO_0003002)) +Declaration(AnnotationProperty(obo:OMO_0003003)) +Declaration(AnnotationProperty(obo:OMO_0003004)) +Declaration(AnnotationProperty(obo:OMO_0003005)) +Declaration(AnnotationProperty(obo:OMO_0003006)) +Declaration(AnnotationProperty(obo:OMO_0003007)) +Declaration(AnnotationProperty(obo:OMO_0003008)) +Declaration(AnnotationProperty(obo:OMO_0003009)) +Declaration(AnnotationProperty(obo:OMO_0003010)) +Declaration(AnnotationProperty(obo:OMO_0003011)) +Declaration(AnnotationProperty(obo:OMO_0003012)) +Declaration(AnnotationProperty(obo:OMO_0003014)) +Declaration(AnnotationProperty(obo:OMO_0004000)) Declaration(AnnotationProperty(obo:RO_0001900)) Declaration(AnnotationProperty(dc:contributor)) Declaration(AnnotationProperty(dc:coverage)) @@ -407,6 +429,7 @@ Declaration(AnnotationProperty(dc:description)) Declaration(AnnotationProperty(dc:format)) Declaration(AnnotationProperty(dc:identifier)) Declaration(AnnotationProperty(dc:language)) +Declaration(AnnotationProperty(dc:license)) Declaration(AnnotationProperty(dc:member)) Declaration(AnnotationProperty(dc:publisher)) Declaration(AnnotationProperty(dc:relation)) @@ -415,10 +438,15 @@ Declaration(AnnotationProperty(dc:source)) Declaration(AnnotationProperty(dc:subject)) Declaration(AnnotationProperty(dc:title)) Declaration(AnnotationProperty(dc:type)) +Declaration(AnnotationProperty(terms:contributor)) +Declaration(AnnotationProperty(terms:created)) Declaration(AnnotationProperty(terms:license)) +Declaration(AnnotationProperty(terms:source)) +Declaration(AnnotationProperty(oboInOwl:SynonymTypeProperty)) Declaration(AnnotationProperty(oboInOwl:created_by)) Declaration(AnnotationProperty(oboInOwl:creation_date)) Declaration(AnnotationProperty(oboInOwl:hasBroadSynonym)) +Declaration(AnnotationProperty(oboInOwl:hasDbXref)) Declaration(AnnotationProperty(oboInOwl:hasExactSynonym)) Declaration(AnnotationProperty(oboInOwl:hasNarrowSynonym)) Declaration(AnnotationProperty(oboInOwl:hasRelatedSynonym)) @@ -429,6 +457,7 @@ Declaration(AnnotationProperty(rdfs:seeAlso)) Declaration(AnnotationProperty(foaf:homepage)) Declaration(AnnotationProperty(foaf:mbox)) Declaration(AnnotationProperty(foaf:page)) +Declaration(Datatype(xsd:date)) ############################ # Annotation Properties ############################ @@ -508,7 +537,7 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000115 "PERSON:Daniel Schober"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000115 "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy obo:IAO_0000115 obo:iao.owl) @@ -544,6 +573,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000118 "OBO Operations committee") AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000118 "PERSON:Daniel Schober"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000118 "GROUP:OBI:"@en) AnnotationAssertion(rdfs:comment obo:IAO_0000118 "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") +AnnotationAssertion(rdfs:isDefinedBy obo:IAO_0000118 obo:iao.owl) AnnotationAssertion(rdfs:label obo:IAO_0000118 "alternative label"@en) # Annotation Property: obo:IAO_0000119 (definition source) @@ -577,13 +607,14 @@ AnnotationAssertion(rdfs:label obo:IAO_0000232 "curator note"@en) # Annotation Property: obo:IAO_0000233 (term tracker item) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000233 "term tracker item"@en) -AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000233 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) +AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000233 "the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588"@en) AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000233 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000233 "An IRI or similar locator for a request or discussion of an ontology term."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000233 "A URL for a request or discussion of an ontology term."@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000233 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000233 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) AnnotationAssertion(rdfs:comment obo:IAO_0000233 "The 'tracker item' can associate a tracker with a specific ontology term."@en) AnnotationAssertion(rdfs:label obo:IAO_0000233 "term tracker item"@en) +AnnotationPropertyRange(obo:IAO_0000233 xsd:anyURI) # Annotation Property: obo:IAO_0000234 (ontology term requester) @@ -837,10 +868,164 @@ AnnotationAssertion(dc:contributor obo:OMO_0002000 ) AnnotationAssertion(rdfs:label obo:OMO_0002000 "defined by construct") +# Annotation Property: obo:OMO_0002001 (preferred label for community) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0002001 "The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease \"A\" and another one \"B\" (but they are the same thing).") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0002001 "A provenance property that denotes a synonym to be the preferred one for a specific community.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0002001 ) +AnnotationAssertion(terms:contributor obo:OMO_0002001 ) +AnnotationAssertion(terms:created obo:OMO_0002001 "2025-06-02"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0002001 "preferred label for community") + +# Annotation Property: obo:OMO_0003000 (abbreviation) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003000 "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003000 "A synonym type for describing abbreviations or initialisms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003000 ) +AnnotationAssertion(terms:contributor obo:OMO_0003000 ) +AnnotationAssertion(terms:created obo:OMO_0003000 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003000 "abbreviation") +SubAnnotationPropertyOf(obo:OMO_0003000 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003001 (ambiguous synonym) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003001 "A synonym type for describing ambiguous synonyms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003001 ) +AnnotationAssertion(terms:contributor obo:OMO_0003001 ) +AnnotationAssertion(terms:created obo:OMO_0003001 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003001 "ambiguous synonym") +SubAnnotationPropertyOf(obo:OMO_0003001 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003002 (dubious synonym) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003002 "A synonym type for describing dubious synonyms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003002 ) +AnnotationAssertion(terms:contributor obo:OMO_0003002 ) +AnnotationAssertion(terms:created obo:OMO_0003002 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003002 "dubious synonym") +SubAnnotationPropertyOf(obo:OMO_0003002 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003003 (layperson synonym) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003003 "EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003003 "A synonym type for describing layperson or colloquial synonyms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003003 ) +AnnotationAssertion(terms:contributor obo:OMO_0003003 ) +AnnotationAssertion(terms:created obo:OMO_0003003 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003003 "layperson synonym") +SubAnnotationPropertyOf(obo:OMO_0003003 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003004 (plural form) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003004 "CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003004 "A synonym type for describing pluralization synonyms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003004 ) +AnnotationAssertion(terms:contributor obo:OMO_0003004 ) +AnnotationAssertion(terms:created obo:OMO_0003004 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003004 "plural form") +SubAnnotationPropertyOf(obo:OMO_0003004 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003005 (UK spelling synonym) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003005 "CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003005 "A synonym type for describing UK spelling variants") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003005 ) +AnnotationAssertion(terms:contributor obo:OMO_0003005 ) +AnnotationAssertion(terms:created obo:OMO_0003005 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003005 "UK spelling synonym") +SubAnnotationPropertyOf(obo:OMO_0003005 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003006 (misspelling) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003006 "A synonym type for common misspellings") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003006 ) +AnnotationAssertion(terms:contributor obo:OMO_0003006 ) +AnnotationAssertion(terms:created obo:OMO_0003006 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003006 "misspelling") +SubAnnotationPropertyOf(obo:OMO_0003006 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003007 (misnomer) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003007 "A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003007 ) +AnnotationAssertion(terms:contributor obo:OMO_0003007 ) +AnnotationAssertion(terms:created obo:OMO_0003007 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003007 "misnomer") +SubAnnotationPropertyOf(obo:OMO_0003007 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003008 (previous name) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003008 "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003008 "A synonym type for names that have been used as primary labels in the past.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003008 ) +AnnotationAssertion(terms:contributor obo:OMO_0003008 ) +AnnotationAssertion(terms:created obo:OMO_0003008 "2023-07-25"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003008 "previous name") +SubAnnotationPropertyOf(obo:OMO_0003008 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003009 (legal name) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003009 "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003009 "A synonym type for the legal entity name") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003009 ) +AnnotationAssertion(terms:contributor obo:OMO_0003009 ) +AnnotationAssertion(terms:created obo:OMO_0003009 "2023-07-27"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003009 "legal name") +SubAnnotationPropertyOf(obo:OMO_0003009 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003010 (International Nonproprietary Name) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003010 "CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) \"paracetamol\". In some cases such as this one, the INN might be the same as the ontology's primary label") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003010 "The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003010 ) +AnnotationAssertion(terms:contributor obo:OMO_0003010 ) +AnnotationAssertion(terms:created obo:OMO_0003010 "2023-09-30"^^xsd:date) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:OMO_0003010 "INN") +AnnotationAssertion(rdfs:label obo:OMO_0003010 "International Nonproprietary Name") +SubAnnotationPropertyOf(obo:OMO_0003010 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003011 (latin term) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003011 "nasopharynx (UBERON:0001728) has the latin name \"pars nasalis pharyngis") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003011 "A synonym type for describing Latin term synonyms.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003011 ) +AnnotationAssertion(terms:contributor obo:OMO_0003011 ) +AnnotationAssertion(terms:created obo:OMO_0003011 "2023-10-12"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003011 "latin term") +SubAnnotationPropertyOf(obo:OMO_0003011 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003012 (acronym) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003012 "NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003012 "A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003012 ) +AnnotationAssertion(terms:contributor obo:OMO_0003012 ) +AnnotationAssertion(terms:created obo:OMO_0003012 "2023-11-01"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003012 "acronym") +SubAnnotationPropertyOf(obo:OMO_0003012 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003014 (has ontology hierarchical property) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003014 "The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: ` a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`.") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003014 "Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003014 ) +AnnotationAssertion(terms:contributor obo:OMO_0003014 ) +AnnotationAssertion(terms:created obo:OMO_0003014 "2025-09-17"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003014 "has ontology hierarchical property") + +# Annotation Property: obo:OMO_0004000 (has symbol) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0004000 "A serial number such as \"12324X\"; a stop sign; a written proper name such as \"OBI") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0004000 "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0004000 ) +AnnotationAssertion(terms:contributor obo:OMO_0004000 ) +AnnotationAssertion(terms:created obo:OMO_0004000 "2024-03-25"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0004000 "has symbol") + # 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"@en) +AnnotationAssertion(rdfs:label obo:RO_0001900 "temporal interpretation") # Annotation Property: oboInOwl:hasBroadSynonym (has broad synonym) @@ -851,6 +1036,15 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has broad synonym"@en) AnnotationAssertion(rdfs:seeAlso oboInOwl:hasBroadSynonym "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") SubAnnotationPropertyOf(oboInOwl:hasBroadSynonym obo:IAO_0000118) +# Annotation Property: oboInOwl:hasDbXref (has cross-reference) + +AnnotationAssertion(obo:IAO_0000112 oboInOwl:hasDbXref "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string") +AnnotationAssertion(obo:IAO_0000115 oboInOwl:hasDbXref "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.") +AnnotationAssertion(obo:IAO_0000233 oboInOwl:hasDbXref ) +AnnotationAssertion(terms:contributor oboInOwl:hasDbXref ) +AnnotationAssertion(terms:created oboInOwl:hasDbXref "2024-03-18"^^xsd:date) +AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "has cross-reference") + # Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) AnnotationAssertion(obo:IAO_0000115 oboInOwl:hasExactSynonym "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") @@ -970,6 +1164,17 @@ AnnotationAssertion(rdfs:comment obo:BFO_0000067 "Paraphrase of definition: a re AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000067 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000067 "contains process"@en) +# Object Property: obo:IAO_0000011 (is directed towards) + +AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000011 "One of my mental representations is directed towards the Pacific Ocean."@en) +AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000011 obo:IAO_0000125) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000011 "A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000011 "person: William Hogan"@en) +AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000011 "https://ceur-ws.org/Vol-1515/regular10.pdf") +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000011 ) +AnnotationAssertion(rdfs:comment obo:IAO_0000011 "In the definition source, the relation is called 'is_about'. To avoid confusion with the existing \"is about\" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion."@en) +AnnotationAssertion(rdfs:label obo:IAO_0000011 "is directed towards"@en) + # Object Property: obo:IAO_0000039 (has measurement unit label) AnnotationAssertion(rdfs:label obo:IAO_0000039 "has measurement unit label"@en) @@ -1209,56 +1414,53 @@ SubObjectPropertyOf(obo:IAO_0000583 obo:BFO_0000051) ObjectPropertyDomain(obo:IAO_0000583 obo:IAO_0000582) ObjectPropertyRange(obo:IAO_0000583 ObjectIntersectionOf(obo:IAO_0000109 ObjectComplementOf(obo:IAO_0000416))) -# Object Property: obo:OBI_0000293 (has_specified_input) +# Object Property: obo:OBI_0000293 (has specified input) -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000293 "has_specified_input") -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000293 "has_specified_input"@en) +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000293 "has specified input") AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000293 "see is_input_of example_of_usage"@en) AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000293 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000293 "The inverse property of is_specified_input_of"@en) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000293 "The inverse property of is specified input of") AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000293 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Bjoern Peters") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Larry Hunter") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Melanie Coutot") AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000293 obo:obi.owl) -AnnotationAssertion(rdfs:label obo:OBI_0000293 "has_specified_input"@en) -EquivalentObjectProperties(obo:OBI_0000293 ObjectInverseOf(obo:OBI_0000295)) +AnnotationAssertion(rdfs:label obo:OBI_0000293 "has specified input"@en) SubObjectPropertyOf(obo:OBI_0000293 obo:RO_0000057) -ObjectPropertyDomain(obo:OBI_0000293 obo:OBI_0000011) +InverseObjectProperties(obo:OBI_0000293 obo:OBI_0000295) +ObjectPropertyDomain(obo:OBI_0000293 obo:COB_0000035) -# Object Property: obo:OBI_0000295 (is_specified_input_of) +# Object Property: obo:OBI_0000295 (is specified input of) -AnnotationAssertion(rdfs:label obo:OBI_0000295 "is_specified_input_of"@en) +AnnotationAssertion(rdfs:label obo:OBI_0000295 "is specified input of"@en) -# Object Property: obo:OBI_0000299 (has_specified_output) +# Object Property: obo:OBI_0000299 (has specified output) -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000299 "has_specified_output") -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000299 "has_specified_output"@en) +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000299 "has specified output") AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000299 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000299 "The inverse property of is_specified_output_of"@en) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000299 "The inverse property of is specified output of") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Bjoern Peters") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Larry Hunter") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Melanie Courtot") AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000299 obo:obi.owl) -AnnotationAssertion(rdfs:label obo:OBI_0000299 "has_specified_output"@en) -EquivalentObjectProperties(obo:OBI_0000299 ObjectInverseOf(obo:OBI_0000312)) +AnnotationAssertion(rdfs:label obo:OBI_0000299 "has specified output"@en) SubObjectPropertyOf(obo:OBI_0000299 obo:RO_0000057) -ObjectPropertyDomain(obo:OBI_0000299 obo:OBI_0000011) +InverseObjectProperties(obo:OBI_0000299 obo:OBI_0000312) +ObjectPropertyDomain(obo:OBI_0000299 obo:COB_0000035) -# Object Property: obo:OBI_0000312 (is_specified_output_of) +# Object Property: obo:OBI_0000312 (is specified output of) -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000312 "is_specified_output_of") -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000312 "is_specified_output_of"@en) +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000312 "is specified output of") AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000312 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000312 "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000312 "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000312 "Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000312 "PERSON:Bjoern Peters") AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000312 obo:obi.owl) -AnnotationAssertion(rdfs:label obo:OBI_0000312 "is_specified_output_of"@en) +AnnotationAssertion(rdfs:label obo:OBI_0000312 "is specified output of"@en) SubObjectPropertyOf(obo:OBI_0000312 obo:RO_0000056) -ObjectPropertyRange(obo:OBI_0000312 obo:OBI_0000011) +ObjectPropertyRange(obo:OBI_0000312 obo:COB_0000035) # Object Property: obo:RO_0000052 (characteristic of) @@ -1309,7 +1511,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:RO_0000057 "this process has participant AnnotationAssertion(obo:IAO_0000115 obo:RO_0000057 "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion(obo:IAO_0000116 obo:RO_0000057 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) AnnotationAssertion(obo:IAO_0000118 obo:RO_0000057 "has_participant"@en) -AnnotationAssertion(dc:source obo:RO_0000057 "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion(terms:source obo:RO_0000057 "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label obo:RO_0000057 "has participant"@en) ObjectPropertyDomain(obo:RO_0000057 obo:BFO_0000003) ObjectPropertyRange(obo:RO_0000057 obo:BFO_0000002) @@ -1318,19 +1520,19 @@ ObjectPropertyRange(obo:RO_0000057 obo:BFO_0000002) AnnotationAssertion(obo:IAO_0000112 obo:RO_0000058 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) AnnotationAssertion(obo:IAO_0000112 obo:RO_0000058 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0000058 "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000058 "A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes."@en) AnnotationAssertion(rdfs:label obo:RO_0000058 "is concretized as"@en) InverseObjectProperties(obo:RO_0000058 obo:RO_0000059) ObjectPropertyDomain(obo:RO_0000058 obo:BFO_0000031) -ObjectPropertyRange(obo:RO_0000058 obo:BFO_0000020) +ObjectPropertyRange(obo:RO_0000058 ObjectUnionOf(obo:BFO_0000015 obo:BFO_0000020)) # Object Property: obo:RO_0000059 (concretizes) AnnotationAssertion(obo:IAO_0000112 obo:RO_0000059 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) AnnotationAssertion(obo:IAO_0000112 obo:RO_0000059 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0000059 "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000059 "A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant."@en) AnnotationAssertion(rdfs:label obo:RO_0000059 "concretizes"@en) -ObjectPropertyDomain(obo:RO_0000059 obo:BFO_0000020) +ObjectPropertyDomain(obo:RO_0000059 ObjectUnionOf(obo:BFO_0000015 obo:BFO_0000020)) ObjectPropertyRange(obo:RO_0000059 obo:BFO_0000031) # Object Property: obo:RO_0000079 (function of) @@ -1461,7 +1663,7 @@ AnnotationAssertion(obo:IAO_0000116 obo:RO_0001025 "Location as a relation betwe AnnotationAssertion(obo:IAO_0000116 obo:RO_0001025 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) AnnotationAssertion(obo:IAO_0000118 obo:RO_0001025 "located_in"@en) AnnotationAssertion(obo:RO_0001900 obo:RO_0001025 obo:RO_0001901) -AnnotationAssertion(dc:source obo:RO_0001025 "http://www.obofoundry.org/ro/#OBO_REL:located_in") +AnnotationAssertion(terms:source obo:RO_0001025 "http://www.obofoundry.org/ro/#OBO_REL:located_in") AnnotationAssertion(rdfs:label obo:RO_0001025 "located in"@en) TransitiveObjectProperty(obo:RO_0001025) ObjectPropertyDomain(Annotation(obo:IAO_0000116 "This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.") obo:RO_0001025 obo:BFO_0000004) @@ -1575,8 +1777,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000008 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000119 obo:APOLLO_SV_00000008 "http://en.wikipedia.org/wiki/Software_development") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000008 "A planned process resulting in a software product involving the creation of source code."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000008 "software development"@en) -EquivalentClasses(obo:APOLLO_SV_00000008 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectUnionOf(obo:IAO_0000010 obo:IAO_0000096)))) -SubClassOf(obo:APOLLO_SV_00000008 obo:OBI_0000011) +EquivalentClasses(obo:APOLLO_SV_00000008 ObjectIntersectionOf(obo:COB_0000035 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectUnionOf(obo:IAO_0000010 obo:IAO_0000096)))) +SubClassOf(obo:APOLLO_SV_00000008 obo:COB_0000035) # Class: obo:APOLLO_SV_00000032 (count) @@ -1594,8 +1796,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000033 "Mathias Brochhausen" AnnotationAssertion(obo:IAO_0000119 obo:APOLLO_SV_00000033 "http://en.wikipedia.org/wiki/Counting") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000033 "The planned process of finding the number of elements in a finite set of objects."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000033 "counting"@en) -EquivalentClasses(obo:APOLLO_SV_00000033 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 obo:APOLLO_SV_00000032))) -SubClassOf(obo:APOLLO_SV_00000033 obo:OBI_0000011) +EquivalentClasses(obo:APOLLO_SV_00000033 ObjectIntersectionOf(obo:COB_0000035 ObjectSomeValuesFrom(obo:OBI_0000299 obo:APOLLO_SV_00000032))) +SubClassOf(obo:APOLLO_SV_00000033 obo:COB_0000035) # Class: obo:APOLLO_SV_00000522 (source code repository) @@ -1627,8 +1829,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000796 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000796 "data set creation"@en) AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000796 "dataset creation"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000796 "dataset creating"@en) -EquivalentClasses(obo:APOLLO_SV_00000796 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000100))) -SubClassOf(obo:APOLLO_SV_00000796 obo:OBI_0000011) +EquivalentClasses(obo:APOLLO_SV_00000796 ObjectIntersectionOf(obo:COB_0000035 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000100))) +SubClassOf(obo:APOLLO_SV_00000796 obo:COB_0000035) # Class: obo:BFO_0000001 (entity) @@ -1705,6 +1907,7 @@ AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000004 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000004 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000004 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:comment obo:BFO_0000004 "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000004 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000004 "independent continuant"@en) SubClassOf(obo:BFO_0000004 obo:BFO_0000002) @@ -1794,6 +1997,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000015 "your process of aging."@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000115 obo:BFO_0000015 "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000015 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000015 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:comment obo:BFO_0000015 "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000015 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000015 "process"@en) SubClassOf(obo:BFO_0000015 obo:BFO_0000003) @@ -1882,6 +2086,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the smell of this portion o AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000115 obo:BFO_0000020 "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) Annotation(rdfs:comment "per discussion with Barry Smith") obo:IAO_0000116 obo:BFO_0000020 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000020 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:comment obo:BFO_0000020 "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000020 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000020 "specifically dependent continuant"@en) SubClassOf(obo:BFO_0000020 obo:BFO_0000002) @@ -2033,6 +2238,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000031 "the pdf file on your laptop AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000031 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000115 obo:BFO_0000031 "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000031 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ") +AnnotationAssertion(rdfs:comment obo:BFO_0000031 "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000031 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000031 "generically dependent continuant"@en) SubClassOf(obo:BFO_0000031 obo:BFO_0000002) @@ -2225,6 +2431,21 @@ AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000182 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000182 "history"@en) SubClassOf(obo:BFO_0000182 obo:BFO_0000015) +# Class: obo:COB_0000035 (completely executed planned process) + +AnnotationAssertion(obo:IAO_0000111 obo:COB_0000035 "completely executed planned process"@en) +AnnotationAssertion(obo:IAO_0000412 obo:COB_0000035 obo:cob.owl) +AnnotationAssertion(rdfs:label obo:COB_0000035 "completely executed planned process"@en) +SubClassOf(obo:COB_0000035 obo:COB_0000082) + +# Class: obo:COB_0000082 (planned process) + +AnnotationAssertion(obo:IAO_0000111 obo:COB_0000082 "planned process"@en) +AnnotationAssertion(obo:IAO_0000115 obo:COB_0000082 "A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification."@en) +AnnotationAssertion(obo:IAO_0000412 obo:COB_0000082 obo:cob.owl) +AnnotationAssertion(rdfs:label obo:COB_0000082 "planned process"@en) +SubClassOf(obo:COB_0000082 obo:BFO_0000015) + # Class: obo:IAO_0000001 (conditional specification) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000001 "conditional specification"@en) @@ -2432,12 +2653,12 @@ AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000025 "group:OBI"@en) AnnotationAssertion(rdfs:label obo:IAO_0000025 "programming language"@en) SubClassOf(obo:IAO_0000025 obo:IAO_0000104) -# Class: obo:IAO_0000027 (data item) +# Class: obo:IAO_0000027 (data entity) -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000027 "data item"@en) +AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000027 "data entity"@en) AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000027 "Data items include counts of things, analyte concentrations, and statistical summaries."@en) AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000027 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000027 "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000027 "An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000027 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000027 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000027 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) @@ -2453,7 +2674,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000027 "PERSON: Alan Ruttenberg"@en AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000027 "PERSON: Chris Stoeckert"@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000027 "PERSON: Jonathan Rees"@en) AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000027 "data"@en) -AnnotationAssertion(rdfs:label obo:IAO_0000027 "data item"@en) +AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000027 "data item"@en) +AnnotationAssertion(rdfs:label obo:IAO_0000027 "data entity"@en) SubClassOf(obo:IAO_0000027 obo:IAO_0000030) # Class: obo:IAO_0000028 (symbol) @@ -2799,12 +3021,13 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000098 "PERSON: Alan Ruttenberg"@en AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000098 "PlanAndPlannedProcess Branch"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000098 "OBI branch derived"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000098 "OBI_0000187"@en) +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000098 ) AnnotationAssertion(rdfs:label obo:IAO_0000098 "data format specification"@en) SubClassOf(obo:IAO_0000098 obo:IAO_0000033) -# Class: obo:IAO_0000100 (data set) +# Class: obo:IAO_0000100 (homogenous data collection) -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000100 "data set"@en) +AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000100 "homogenous data collection"@en) AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000100 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en) AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000100 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000100 "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en) @@ -2812,10 +3035,10 @@ AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000100 "2009/10/23 Alan Ruttenberg. AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000100 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.") AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000100 "person:Allyson Lister"@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000100 "person:Chris Stoeckert"@en) -AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000100 "OBI_0000042"@en) +AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000100 "data set"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000100 "group:OBI"@en) -AnnotationAssertion(rdfs:label obo:IAO_0000100 "data set"@en) -SubClassOf(obo:IAO_0000100 obo:IAO_0000027) +AnnotationAssertion(rdfs:label obo:IAO_0000100 "homogenous data collection"@en) +SubClassOf(obo:IAO_0000100 obo:IAO_0001000) # Class: obo:IAO_0000101 (image) @@ -3618,7 +3841,7 @@ AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000443 obo:IAO_0000120) AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000443 "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing") AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000443 "Person:Alan Ruttenberg") AnnotationAssertion(rdfs:label obo:IAO_0000443 "data item extraction from journal article") -SubClassOf(obo:IAO_0000443 obo:OBI_0000011) +SubClassOf(obo:IAO_0000443 obo:COB_0000035) SubClassOf(obo:IAO_0000443 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000013)) SubClassOf(obo:IAO_0000443 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000027)) @@ -3631,7 +3854,7 @@ AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000444 "https://en.wikipedia.org/wi AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000444 ) AnnotationAssertion(obo:IAO_0000234 obo:IAO_0000444 "VEuPathDB"@en) AnnotationAssertion(rdfs:label obo:IAO_0000444 "publishing process"@en) -SubClassOf(obo:IAO_0000444 obo:OBI_0000011) +SubClassOf(obo:IAO_0000444 obo:COB_0000035) # Class: obo:IAO_0000445 (document in preparation for publication) @@ -3653,7 +3876,7 @@ AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000572 "6/11/9: Edited at OBI works AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000572 "Bjoern Peters"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000572 "wikipedia http://en.wikipedia.org/wiki/Documenting"@en) AnnotationAssertion(rdfs:label obo:IAO_0000572 "documenting"@en) -SubClassOf(obo:IAO_0000572 obo:OBI_0000011) +SubClassOf(obo:IAO_0000572 obo:COB_0000035) SubClassOf(obo:IAO_0000572 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000030)) SubClassOf(obo:IAO_0000572 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000310)) @@ -3682,7 +3905,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000574 "Person:Bjoern Peters"@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000574 "Person:Melanie Courtot"@en) AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000574 "assigning a CRID") AnnotationAssertion(rdfs:label obo:IAO_0000574 "assigning a centrally registered identifier"@en) -SubClassOf(obo:IAO_0000574 obo:OBI_0000011) +SubClassOf(obo:IAO_0000574 obo:COB_0000035) SubClassOf(obo:IAO_0000574 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000577)) SubClassOf(obo:IAO_0000574 ObjectSomeValuesFrom(obo:RO_0000057 obo:IAO_0000579)) @@ -3694,7 +3917,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000575 "A planned process in which AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000575 "PERSON:Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000575 "associating information with a CRID in the CRID registry") AnnotationAssertion(rdfs:label obo:IAO_0000575 "associating information with a centrally registered identifier in its registry"@en) -SubClassOf(obo:IAO_0000575 obo:OBI_0000011) +SubClassOf(obo:IAO_0000575 obo:COB_0000035) SubClassOf(obo:IAO_0000575 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000030)) SubClassOf(obo:IAO_0000575 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000577)) SubClassOf(obo:IAO_0000575 ObjectSomeValuesFrom(obo:RO_0000057 obo:IAO_0000579)) @@ -3769,7 +3992,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000580 "PERSON: Bjoern Peters"@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000580 "PERSON: Melanie Courtot"@en) AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000580 "looking up a CRID") AnnotationAssertion(rdfs:label obo:IAO_0000580 "looking up a centrally registered identifier"@en) -SubClassOf(obo:IAO_0000580 obo:OBI_0000011) +SubClassOf(obo:IAO_0000580 obo:COB_0000035) SubClassOf(obo:IAO_0000580 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000577)) SubClassOf(obo:IAO_0000580 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000030)) SubClassOf(obo:IAO_0000580 ObjectSomeValuesFrom(obo:RO_0000057 obo:IAO_0000579)) @@ -4471,10 +4694,19 @@ AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000650 ) AnnotationAssertion(rdfs:label obo:IAO_0000650 "database extract, transform, and load process"@en) AnnotationAssertion(foaf:page obo:IAO_0000650 ) -SubClassOf(obo:IAO_0000650 obo:OBI_0000011) +SubClassOf(obo:IAO_0000650 obo:COB_0000035) SubClassOf(obo:IAO_0000650 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000030)) SubClassOf(obo:IAO_0000650 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000030)) +# Class: obo:IAO_0000651 (title section) + +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000651 "the section of the document where the title appears"@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000651 "This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000651 "Charles Tapley Hoyt"@en) +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000651 "https://github.com/information-artifact-ontology/IAO/issues/286"^^xsd:anyURI) +AnnotationAssertion(rdfs:label obo:IAO_0000651 "title section"@en) +SubClassOf(obo:IAO_0000651 obo:IAO_0000314) + # Class: obo:IAO_0000701 (descriptive data section) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000701 "descriptive data section"@en) @@ -4587,6 +4819,17 @@ AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000708 "https://github.com/informat AnnotationAssertion(rdfs:label obo:IAO_0000708 "ORCID identifier"@en) SubClassOf(obo:IAO_0000708 obo:IAO_0000578) +# Class: obo:IAO_0001000 (data collection) + +AnnotationAssertion(obo:IAO_0000111 obo:IAO_0001000 "data collection"@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0001000 "A data entity that consists of multiple data entities."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IAO_0001000 "Sebastian Duesing") +AnnotationAssertion(obo:IAO_0000118 obo:IAO_0001000 "data set"@en) +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0001000 "https://github.com/information-artifact-ontology/IAO/issues/283") +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0001000 "https://github.com/obi-ontology/obi/issues/1877") +AnnotationAssertion(rdfs:label obo:IAO_0001000 "data collection"@en) +SubClassOf(obo:IAO_0001000 obo:IAO_0000027) + # Class: obo:IAO_0020000 (identifier) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0020000 "identifier"@en) @@ -4623,8 +4866,8 @@ AnnotationAssertion(obo:IAO_0000118 obo:IAO_0020010 "naming"@en) AnnotationAssertion(obo:IAO_0000233 obo:IAO_0020010 "https://github.com/information-artifact-ontology/IAO/issues/237"@en) AnnotationAssertion(dc:creator obo:IAO_0020010 "Mathias Brochhausen") AnnotationAssertion(rdfs:label obo:IAO_0020010 "identifier creating process"@en) -EquivalentClasses(obo:IAO_0020010 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0020000))) -SubClassOf(obo:IAO_0020010 obo:OBI_0000011) +EquivalentClasses(obo:IAO_0020010 ObjectIntersectionOf(obo:COB_0000035 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0020000))) +SubClassOf(obo:IAO_0020010 obo:COB_0000035) # Class: obo:IAO_0020015 (personal name) @@ -4875,42 +5118,34 @@ AnnotationAssertion(obo:IAO_0000111 obo:IAO_8000020 "EL++ ontology module"@en) AnnotationAssertion(rdfs:label obo:IAO_8000020 "EL++ ontology module"@en) SubClassOf(obo:IAO_8000020 obo:IAO_8000019) -# Class: obo:OBI_0000011 (planned process) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000011 "planned process"@en) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000011 "A process that realizes a plan which is the concretization of a plan specification."@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000011 obo:obi.owl) -AnnotationAssertion(rdfs:label obo:OBI_0000011 "planned process"@en) -SubClassOf(obo:OBI_0000011 obo:BFO_0000015) - # Class: obo:OBI_0000066 (investigation) AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000066 "investigation"@en) AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000066 "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)."@en) AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000066 obo:obi.owl) AnnotationAssertion(rdfs:label obo:OBI_0000066 "investigation"@en) -SubClassOf(obo:OBI_0000066 obo:OBI_0000011) +SubClassOf(obo:OBI_0000066 obo:COB_0000035) # Class: obo:OBI_0000471 (study design execution) AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000471 "study design execution") -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000471 "a planned process that carries out a study design") +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000471 "a planned process that carries out a study design"@en) AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000471 obo:obi.owl) AnnotationAssertion(rdfs:label obo:OBI_0000471 "study design execution") -SubClassOf(obo:OBI_0000471 obo:OBI_0000011) +SubClassOf(obo:OBI_0000471 obo:COB_0000035) # Class: obo:OBI_0200000 (data transformation) AnnotationAssertion(obo:IAO_0000111 obo:OBI_0200000 "data transformation"@en) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200000 "A planned process that produces output data from input data."@en) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200000 "A completely executed planned process that produces output data from input data."@en) AnnotationAssertion(obo:IAO_0000412 obo:OBI_0200000 obo:obi.owl) AnnotationAssertion(rdfs:label obo:OBI_0200000 "data transformation"@en) -SubClassOf(obo:OBI_0200000 obo:OBI_0000011) +SubClassOf(obo:OBI_0200000 obo:COB_0000035) # Class: obo:OBI_0500000 (study design) AnnotationAssertion(obo:IAO_0000111 obo:OBI_0500000 "study design"@en) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0500000 "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.") +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0500000 "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution."@en) AnnotationAssertion(obo:IAO_0000412 obo:OBI_0500000 obo:obi.owl) AnnotationAssertion(rdfs:label obo:OBI_0500000 "study design"@en) SubClassOf(obo:OBI_0500000 obo:IAO_0000104) @@ -4958,6 +5193,7 @@ SubClassOf(obo:PATO_0001241 obo:BFO_0000019) # Class: obo:UO_0000001 (length unit) AnnotationAssertion(obo:IAO_0000111 obo:UO_0000001 "length unit") +AnnotationAssertion(obo:IAO_0000115 obo:UO_0000001 "A unit which is a standard measure of the distance between two points.") AnnotationAssertion(obo:IAO_0000412 obo:UO_0000001 obo:uo.owl) AnnotationAssertion(rdfs:label obo:UO_0000001 "length unit") SubClassOf(obo:UO_0000001 obo:IAO_0000003) @@ -4965,6 +5201,7 @@ SubClassOf(obo:UO_0000001 obo:IAO_0000003) # Class: obo:UO_0000002 (mass unit) AnnotationAssertion(obo:IAO_0000111 obo:UO_0000002 "mass unit") +AnnotationAssertion(obo:IAO_0000115 obo:UO_0000002 "A unit which is a standard measure of the amount of matter/energy of a physical object.") AnnotationAssertion(obo:IAO_0000412 obo:UO_0000002 obo:uo.owl) AnnotationAssertion(rdfs:label obo:UO_0000002 "mass unit") SubClassOf(obo:UO_0000002 obo:IAO_0000003) @@ -4972,6 +5209,7 @@ SubClassOf(obo:UO_0000002 obo:IAO_0000003) # Class: obo:UO_0000003 (time unit) AnnotationAssertion(obo:IAO_0000111 obo:UO_0000003 "time unit") +AnnotationAssertion(obo:IAO_0000115 obo:UO_0000003 "A unit which is a standard measure of the dimension in which events occur in sequence.") AnnotationAssertion(obo:IAO_0000412 obo:UO_0000003 obo:uo.owl) AnnotationAssertion(rdfs:label obo:UO_0000003 "time unit") SubClassOf(obo:UO_0000003 obo:IAO_0000003) @@ -4990,8 +5228,11 @@ ClassAssertion(obo:IAO_0000078 obo:IAO_0000002) # Individual: obo:IAO_0000103 (failed exploratory term) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000103 "failed exploratory term"@en) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000103 "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000103 "The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000103 "Terms created as placeholders with the expectation of being permanent should instead be deprecated using the \"placeholder removed\" (obo:IAO_0000226) justification."@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000103 "Person:Alan Ruttenberg"@en) +AnnotationAssertion(dc:contributor obo:IAO_0000103 ) +AnnotationAssertion(dc:contributor obo:IAO_0000103 ) AnnotationAssertion(rdfs:label obo:IAO_0000103 "failed exploratory term"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000103) ClassAssertion(owl:Thing obo:IAO_0000103) @@ -5006,7 +5247,7 @@ ClassAssertion(obo:IAO_0000078 obo:IAO_0000120) # Individual: obo:IAO_0000121 (organizational term) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000121 "organizational term"@en) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000121 "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000121 "The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release."@en) AnnotationAssertion(rdfs:label obo:IAO_0000121 "organizational term"@en) ClassAssertion(obo:IAO_0000078 obo:IAO_0000121) @@ -5050,6 +5291,10 @@ AnnotationAssertion(owl:deprecated obo:IAO_0000224 "true"^^xsd:boolean) # Individual: obo:IAO_0000226 (placeholder removed) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000226 "placeholder removed"@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000226 "The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000226 "This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider."@en) +AnnotationAssertion(dc:contributor obo:IAO_0000226 ) +AnnotationAssertion(dc:contributor obo:IAO_0000226 ) AnnotationAssertion(rdfs:label obo:IAO_0000226 "placeholder removed"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000226) ClassAssertion(owl:Thing obo:IAO_0000226) @@ -5057,21 +5302,30 @@ ClassAssertion(owl:Thing obo:IAO_0000226) # Individual: obo:IAO_0000227 (terms merged) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000227 "terms merged"@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000227 "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000227 "The term has been combined with one or more other terms to create a more encompassing (merged) term."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000227 "The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(dc:contributor obo:IAO_0000227 ) +AnnotationAssertion(dc:contributor obo:IAO_0000227 ) AnnotationAssertion(rdfs:label obo:IAO_0000227 "terms merged"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000227) # Individual: obo:IAO_0000228 (term imported) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000228 "term imported"@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000228 "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000228 "The term has been replaced by a term imported from another ontology."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000228 "This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001."@en) +AnnotationAssertion(dc:contributor obo:IAO_0000228 ) +AnnotationAssertion(dc:contributor obo:IAO_0000228 ) AnnotationAssertion(rdfs:label obo:IAO_0000228 "term imported"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000228) # Individual: obo:IAO_0000229 (term split) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000229 "term split"@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000229 "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000229 "The term has been split into two or more new terms."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000229 "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001."@en) +AnnotationAssertion(dc:contributor obo:IAO_0000229 ) +AnnotationAssertion(dc:contributor obo:IAO_0000229 ) AnnotationAssertion(rdfs:label obo:IAO_0000229 "term split"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000229) @@ -5130,20 +5384,32 @@ ClassAssertion(obo:IAO_0000078 obo:IAO_0000428) # Individual: obo:OMO_0001000 (out of scope) AnnotationAssertion(obo:IAO_0000115 obo:OMO_0001000 "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) -AnnotationAssertion(obo:IAO_0000116 obo:OMO_0001000 "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OMO_0001000 "This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype."@en) AnnotationAssertion(obo:IAO_0000117 obo:OMO_0001000 ) AnnotationAssertion(obo:IAO_0000233 obo:OMO_0001000 "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") AnnotationAssertion(obo:IAO_0000234 obo:OMO_0001000 "https://orcid.org/0000-0001-5208-3432") +AnnotationAssertion(dc:contributor obo:OMO_0001000 ) +AnnotationAssertion(dc:contributor obo:OMO_0001000 ) AnnotationAssertion(rdfs:label obo:OMO_0001000 "out of scope") ClassAssertion(obo:IAO_0000225 obo:OMO_0001000) +# Individual: obo:OMO_0001002 (domain entity does not exist) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0001002 "The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OMO_0001002 "This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). "@en) +AnnotationAssertion(obo:IAO_0000117 obo:OMO_0001002 ) +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0001002 "https://github.com/information-artifact-ontology/ontology-metadata/issues/136") +AnnotationAssertion(obo:IAO_0000234 obo:OMO_0001002 "https://orcid.org/0000-0002-4142-7153") +AnnotationAssertion(rdfs:label obo:OMO_0001002 "domain entity does not exist") +ClassAssertion(obo:IAO_0000225 obo:OMO_0001002) + DifferentIndividuals(obo:IAO_0000120 obo:IAO_0000121 obo:IAO_0000122 obo:IAO_0000123 obo:IAO_0000124 obo:IAO_0000125 obo:IAO_0000423 obo:IAO_0000428) DifferentIndividuals(obo:IAO_0000226 obo:IAO_0000227 obo:IAO_0000228 obo:IAO_0000229) SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000050 obo:BFO_0000066) obo:BFO_0000066) SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000066 obo:BFO_0000050) obo:BFO_0000066) -DLSafeRule(Body(ClassAtom(obo:BFO_0000016 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000091 Variable() Variable()))) -DLSafeRule(Body(ClassAtom(obo:BFO_0000019 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000086 Variable() Variable()))) -DLSafeRule(Body(ClassAtom(obo:BFO_0000023 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000087 Variable() Variable()))) -DLSafeRule(Body(ClassAtom(obo:BFO_0000034 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000085 Variable() Variable()))) +DLSafeRule(Body(ClassAtom(obo:BFO_0000016 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000091 Variable() Variable()))) +DLSafeRule(Body(ClassAtom(obo:BFO_0000019 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000086 Variable() Variable()))) +DLSafeRule(Body(ClassAtom(obo:BFO_0000023 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000087 Variable() Variable()))) +DLSafeRule(Body(ClassAtom(obo:BFO_0000034 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000085 Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl index 5bc462f..1ed694a 100644 --- a/src/ontology/imports/ido_import.owl +++ b/src/ontology/imports/ido_import.owl @@ -1,1792 +1,164 @@ Prefix(:=) +Prefix(dc:=) +Prefix(obo:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) +Prefix(foaf:=) Prefix(rdfs:=) +Prefix(protege:=) +Prefix(oboInOwl:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2026-03-13") - -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty(owl:topObjectProperty)) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty(rdfs:comment)) -Declaration(AnnotationProperty(rdfs:label)) -Declaration(AnnotationProperty()) -############################ -# Annotation Properties -############################ - -# Annotation Property: (BFO OWL specification label) - -AnnotationAssertion( "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification."@en) -AnnotationAssertion( "Really of interest to developers only"@en) -AnnotationAssertion(rdfs:label "BFO OWL specification label"@en) - -# Annotation Property: (BFO CLIF specification label) - -AnnotationAssertion( "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2"@en) -AnnotationAssertion( "Person:Alan Ruttenberg") -AnnotationAssertion( "Really of interest to developers only"@en) -AnnotationAssertion(rdfs:label "BFO CLIF specification label"@en) - -# Annotation Property: (editor preferred term) - -AnnotationAssertion( "editor preferred term"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "editor preferred term"@en) - -# Annotation Property: (example of usage) - -AnnotationAssertion( "example"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "example of usage"@en) - -# Annotation Property: (has curation status) - -AnnotationAssertion( "has curation status"@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Bill Bug"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "OBI_0000281"@en) -AnnotationAssertion(rdfs:label "has curation status"@en) - -# Annotation Property: (definition) - -AnnotationAssertion( "definition"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) -AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) -AnnotationAssertion( "2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "definition") -AnnotationAssertion(rdfs:label "definition"@en) -AnnotationAssertion(rdfs:label "textual definition") - -# Annotation Property: (editor note) - -AnnotationAssertion( "editor note"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "editor note"@en) - -# Annotation Property: (term editor) - -AnnotationAssertion( "term editor"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) -AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "term editor"@en) - -# Annotation Property: (alternative term) - -AnnotationAssertion( "alternative term"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "alternative term"@en) - -# Annotation Property: (definition source) - -AnnotationAssertion( "definition source"@en) -AnnotationAssertion( ) -AnnotationAssertion( "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w") -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "definition source"@en) - -# Annotation Property: (has obsolescence reason) - -AnnotationAssertion( "has obsolescence reason"@en) -AnnotationAssertion( "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification."@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion(rdfs:label "has obsolescence reason"@en) - -# Annotation Property: (curator note) - -AnnotationAssertion( "curator note"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An administrative note of use for a curator but of no use for a user"@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "curator note"@en) - -# Annotation Property: (imported from) - -AnnotationAssertion( "imported from"@en) -AnnotationAssertion( ) -AnnotationAssertion( "For external terms/classes, the ontology from which the term was imported"@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "imported from"@en) - -# Annotation Property: (expand expression to) - -AnnotationAssertion( "expand expression to"@en) -AnnotationAssertion( "ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" -"@en) -AnnotationAssertion( "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones"@en) -AnnotationAssertion( "Chris Mungall") -AnnotationAssertion(rdfs:label "expand expression to"@en) - -# Annotation Property: (OBO foundry unique label) - -AnnotationAssertion( "OBO foundry unique label"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An alternative name for a class or property which is unique across the OBO Foundry."@en) -AnnotationAssertion( "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .") -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Bjoern Peters"@en) -AnnotationAssertion( "PERSON:Chris Mungall"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "GROUP:OBO Foundry "@en) -AnnotationAssertion(rdfs:label "OBO foundry unique label"@en) - -# Annotation Property: (elucidation) - -AnnotationAssertion( "elucidation"@en) -AnnotationAssertion( "person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Barry Smith"@en) -AnnotationAssertion( "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en) -AnnotationAssertion(rdfs:label "elucidation"@en) - -# Annotation Property: (has associated axiom(nl)) - -AnnotationAssertion( "has associated axiom(nl)"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "An axiom associated with a term expressed using natural language"@en) -AnnotationAssertion(rdfs:label "has associated axiom(nl)"@en) - -# Annotation Property: (has associated axiom(fol)) - -AnnotationAssertion( "has associated axiom(fol)"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "An axiom expressed in first order logic using CLIF syntax"@en) -AnnotationAssertion(rdfs:label "has associated axiom(fol)"@en) - -# Annotation Property: (term replaced by) - -AnnotationAssertion( "term replaced by"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Add as annotation triples in the granting ontology"@en) -AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "term replaced by"@en) - -# Annotation Property: (temporal interpretation) - -AnnotationAssertion(rdfs:label "temporal interpretation"@en) -AnnotationAssertion( "https://github.com/oborel/obo-relations/wiki/ROAndTime"^^xsd:anyURI) - -# Annotation Property: (shorthand) - -AnnotationAssertion(rdfs:label "shorthand") - -# Annotation Property: rdfs:label (label) - -AnnotationAssertion(rdfs:label rdfs:label "label") - - -############################ -# Object Properties -############################ - -# Object Property: (part of) - -AnnotationAssertion( "is part of"@en) -AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) -AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) -AnnotationAssertion( "a core relation that holds between a part and its whole"@en) -AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) -AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"@en) -AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) -AnnotationAssertion( "part_of"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "part of"@en) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (has part) - -AnnotationAssertion( "has part"@en) -AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) -AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) -AnnotationAssertion( "a core relation that holds between a whole and its part"@en) -AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) -AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"@en) -AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) -AnnotationAssertion( "has_part"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has part"@en) -SubObjectPropertyOf( owl:topObjectProperty) -TransitiveObjectProperty() - -# Object Property: (realized in) - -AnnotationAssertion( "realized in"@en) -AnnotationAssertion( "this disease is realized in this disease course"@en) -AnnotationAssertion( "this fragility is realized in this shattering"@en) -AnnotationAssertion( "this investigator role is realized in this investigation"@en) -AnnotationAssertion( "is realized by"@en) -AnnotationAssertion( "realized_in"@en) -AnnotationAssertion( "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) -AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") -AnnotationAssertion(rdfs:label "realized in"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (realizes) - -AnnotationAssertion( "realizes"@en) -AnnotationAssertion( "this disease course realizes this disease"@en) -AnnotationAssertion( "this investigation realizes this investigator role"@en) -AnnotationAssertion( "this shattering realizes this fragility"@en) -AnnotationAssertion( "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) -AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") -AnnotationAssertion(rdfs:label "realizes"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (preceded by) - -AnnotationAssertion( "preceded by"@en) -AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) -AnnotationAssertion( "is preceded by"@en) -AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") -AnnotationAssertion(rdfs:label "preceded by"@en) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (precedes) - -AnnotationAssertion( "precedes"@en) -AnnotationAssertion(rdfs:label "precedes"@en) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (occurs in) - -AnnotationAssertion( "occurs in"@en) -AnnotationAssertion( "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) -AnnotationAssertion( "occurs_in"@en) -AnnotationAssertion( "unfolds in"@en) -AnnotationAssertion( "unfolds_in"@en) -AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") -AnnotationAssertion(rdfs:label "occurs in"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (contains process) - -AnnotationAssertion( "site of"@en) -AnnotationAssertion( "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) -AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant") -AnnotationAssertion(rdfs:label "contains process"@en) - -# Object Property: (results_in) - -AnnotationAssertion(rdfs:label "results_in"@en) - -# Object Property: (inheres in) - -AnnotationAssertion( "inheres in"@en) -AnnotationAssertion( "this fragility inheres in this vase"@en) -AnnotationAssertion( "this red color inheres in this apple"@en) -AnnotationAssertion( "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A dependent inheres in its bearer at all times for which the dependent exists."@en) -AnnotationAssertion( "inheres_in"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "inheres in"@en) -InverseObjectProperties( ) - -# Object Property: (bearer of) - -AnnotationAssertion( "bearer of"@en) -AnnotationAssertion( "this apple is bearer of this red color"@en) -AnnotationAssertion( "this vase is bearer of this fragility"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) -AnnotationAssertion( "bearer_of"@en) -AnnotationAssertion( "is bearer of"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "bearer of"@en) -ObjectPropertyRange( ) - -# Object Property: (participates in) - -AnnotationAssertion( "participates in"@en) -AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) -AnnotationAssertion( "this input material (or this output material) participates in this process"@en) -AnnotationAssertion( "this investigator participates in this investigation"@en) -AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "participates_in"@en) -AnnotationAssertion(rdfs:label "participates in"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has participant) - -AnnotationAssertion( "has participant"@en) -AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) -AnnotationAssertion( "this investigation has participant this investigator"@en) -AnnotationAssertion( "this process has participant this input material (or this output material)"@en) -AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) -AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") -AnnotationAssertion(rdfs:label "has participant"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (is concretized as) - -AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) -AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) -AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) -AnnotationAssertion(rdfs:label "is concretized as"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (concretizes) - -AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) -AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) -AnnotationAssertion( "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) -AnnotationAssertion(rdfs:label "concretizes"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (role of) - -AnnotationAssertion( "this investigator role is a role of this person"@en) -AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) -AnnotationAssertion( "is role of"@en) -AnnotationAssertion( "role_of"@en) -AnnotationAssertion(rdfs:label "role of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has role) - -AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) -AnnotationAssertion( "has_role"@en) -AnnotationAssertion(rdfs:label "has role"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has disposition) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has disposition"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (disposition of) - -AnnotationAssertion(rdfs:label "disposition of"@en) -SubObjectPropertyOf( ) - -# Object Property: (location of) - -AnnotationAssertion( "is location of"@en) -AnnotationAssertion( "my head is the location of my brain"@en) -AnnotationAssertion( "this cage is the location of this rat"@en) -AnnotationAssertion( "a relation between two independent continuants, the location and the target, in which the target is entirely within the location"@en) -AnnotationAssertion( "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"@en) -AnnotationAssertion( "location_of"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "location of"@en) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (located in) - -AnnotationAssertion( "located in"@en) -AnnotationAssertion( "my brain is located in my head"@en) -AnnotationAssertion( "this rat is located in this cage"@en) -AnnotationAssertion( "a relation between two independent continuants, the target and the location, in which the target is entirely within the location"@en) -AnnotationAssertion( "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus"@en) -AnnotationAssertion( "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime"@en) -AnnotationAssertion( "located_in"@en) -AnnotationAssertion( ) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:located_in") -AnnotationAssertion(rdfs:label "located in"@en) -TransitiveObjectProperty() - -# Object Property: (regulates) - -AnnotationAssertion( ) -AnnotationAssertion( "x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y") -AnnotationAssertion( "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit") -AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "David Hill") -AnnotationAssertion( "Tanya Berardini") -AnnotationAssertion( ) -AnnotationAssertion( "GO") -AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") -AnnotationAssertion( "regulates (processual)") -AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion(rdfs:label "regulates"@en) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulates) - -AnnotationAssertion( ) -AnnotationAssertion( "x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y") -AnnotationAssertion( "Chris Mungall"@en) -AnnotationAssertion( ) -AnnotationAssertion( "negatively regulates (process to process)") -AnnotationAssertion(rdfs:label "negatively regulates"@en) -SubObjectPropertyOf( ) - -# Object Property: (has output) - -AnnotationAssertion( ) -AnnotationAssertion( "p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.") -AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "produces") -AnnotationAssertion(rdfs:label "has output"@en) -SubObjectPropertyOf( ) - -# Object Property: (results in formation of) - -AnnotationAssertion( "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") -AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "GOC:mtg_berkeley_2013") -AnnotationAssertion( "results_in_formation_of") -AnnotationAssertion(rdfs:label "results in formation of"@en) -SubObjectPropertyOf( ) - -# Object Property: (member of) - -AnnotationAssertion( "An organism that is a member of a population of organisms") -AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") -AnnotationAssertion( "is member of") -AnnotationAssertion( "member part of") -AnnotationAssertion( "SIO") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "member of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has member) - -AnnotationAssertion( "has member is a mereological relation between a collection and an item.") -AnnotationAssertion( "SIO") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has member"@en) -SubObjectPropertyOf( ) -IrreflexiveObjectProperty() - + +Annotation(dc:source ) +Annotation(owl:versionInfo "2026-07-19") + +Declaration(Class(obo:BFO_0000019)) +Declaration(Class(obo:IDO_0000479)) +Declaration(Class(obo:IDO_0000480)) +Declaration(Class(obo:IDO_0000481)) +Declaration(Class(obo:IDO_0000482)) +Declaration(Class(obo:IDO_0000483)) +Declaration(Class(obo:IDO_0000484)) +Declaration(Class(obo:IDO_0000485)) +Declaration(Class(obo:IDO_0000486)) +Declaration(Class(obo:IDO_0000487)) +Declaration(Class(obo:IDO_0000488)) +Declaration(Class(obo:IDO_0000489)) +Declaration(Class(obo:IDO_0000623)) +Declaration(AnnotationProperty(obo:IAO_0000115)) +Declaration(AnnotationProperty(obo:IAO_0000117)) +Declaration(AnnotationProperty(obo:IAO_0000118)) +Declaration(AnnotationProperty(dc:source)) ############################ # Classes ############################ -# Class: (entity) - -AnnotationAssertion( "entity") -AnnotationAssertion( "Entity") -AnnotationAssertion( "Julius Caesar"@en) -AnnotationAssertion( "Verdi’s Requiem"@en) -AnnotationAssertion( "the Second World War"@en) -AnnotationAssertion( "your body mass index"@en) -AnnotationAssertion( "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) -AnnotationAssertion(rdfs:label "entity"@en) - -# Class: (continuant) - -AnnotationAssertion( "continuant") -AnnotationAssertion( "Continuant") -AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) -AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) -AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (occurrent) - -AnnotationAssertion( "occurrent") -AnnotationAssertion( "Occurrent") -AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) -AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) -AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) -AnnotationAssertion(rdfs:label "occurrent"@en) -SubClassOf( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (independent continuant) - -AnnotationAssertion( "ic") -AnnotationAssertion( "IndependentContinuant") -AnnotationAssertion( "a chair"@en) -AnnotationAssertion( "a heart"@en) -AnnotationAssertion( "a leg"@en) -AnnotationAssertion( "a molecule"@en) -AnnotationAssertion( "a spatial region"@en) -AnnotationAssertion( "an atom"@en) -AnnotationAssertion( "an orchestra."@en) -AnnotationAssertion( "an organism"@en) -AnnotationAssertion( "the bottom right portion of a human torso"@en) -AnnotationAssertion( "the interior of your mouth"@en) -AnnotationAssertion( "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) -AnnotationAssertion(rdfs:label "independent continuant"@en) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (spatial region) - -AnnotationAssertion( "s-region") -AnnotationAssertion( "SpatialRegion") -AnnotationAssertion( "BFO 2 Reference: Spatial regions do not participate in processes."@en) -AnnotationAssertion(rdfs:label "spatial region"@en) -SubClassOf( ) - -# Class: (temporal region) - -AnnotationAssertion( "t-region") -AnnotationAssertion( "TemporalRegion") -AnnotationAssertion(rdfs:label "temporal region"@en) -SubClassOf( ) - -# Class: (spatiotemporal region) - -AnnotationAssertion( "st-region") -AnnotationAssertion( "SpatiotemporalRegion") -AnnotationAssertion( "the spatiotemporal region occupied by a human life"@en) -AnnotationAssertion( "the spatiotemporal region occupied by a process of cellular meiosis."@en) -AnnotationAssertion( "the spatiotemporal region occupied by the development of a cancer tumor"@en) -AnnotationAssertion( "Every spatiotemporal region occupies_spatiotemporal_region itself."@en) -AnnotationAssertion(rdfs:label "spatiotemporal region"@en) -SubClassOf( ) - -# Class: (process) - -AnnotationAssertion( "process") -AnnotationAssertion( "Process") -AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) -AnnotationAssertion( "a process of meiosis"@en) -AnnotationAssertion( "a process of sleeping"@en) -AnnotationAssertion( "the course of a disease"@en) -AnnotationAssertion( "the flight of a bird"@en) -AnnotationAssertion( "the life of an organism"@en) -AnnotationAssertion( "your process of aging."@en) -AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) -AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) -AnnotationAssertion(rdfs:label "process"@en) -SubClassOf( ) - -# Class: (disposition) - -AnnotationAssertion( "disposition") -AnnotationAssertion( "Disposition") -AnnotationAssertion( "an atom of element X has the disposition to decay to an atom of element Y"@en) -AnnotationAssertion( "certain people have a predisposition to colon cancer"@en) -AnnotationAssertion( "children are innately disposed to categorize objects in certain ways."@en) -AnnotationAssertion( "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en) -AnnotationAssertion( "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type."@en) -AnnotationAssertion(rdfs:label "disposition"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (realizable entity) - -AnnotationAssertion( "realizable") -AnnotationAssertion( "RealizableEntity") -AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) -AnnotationAssertion( "the disposition of your blood to coagulate"@en) -AnnotationAssertion( "the function of your reproductive organs"@en) -AnnotationAssertion( "the role of being a doctor"@en) -AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) -AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) -AnnotationAssertion(rdfs:label "realizable entity"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (quality) - -AnnotationAssertion( "quality") -AnnotationAssertion( "Quality") -AnnotationAssertion( "the ambient temperature of this portion of air"@en) -AnnotationAssertion( "the color of a tomato"@en) -AnnotationAssertion( "the length of the circumference of your waist"@en) -AnnotationAssertion( "the mass of this piece of gold."@en) -AnnotationAssertion( "the shape of your nose"@en) -AnnotationAssertion( "the shape of your nostril"@en) -AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) - -# Class: (specifically dependent continuant) - -AnnotationAssertion( "sdc") -AnnotationAssertion( "SpecificallyDependentContinuant") -AnnotationAssertion( "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) -AnnotationAssertion( "of one-sided specifically dependent continuants: the mass of this tomato"@en) -AnnotationAssertion( "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) -AnnotationAssertion( "the disposition of this fish to decay"@en) -AnnotationAssertion( "the function of this heart: to pump blood"@en) -AnnotationAssertion( "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) -AnnotationAssertion( "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) -AnnotationAssertion( "the pink color of a medium rare piece of grilled filet mignon at its center"@en) -AnnotationAssertion( "the role of being a doctor"@en) -AnnotationAssertion( "the shape of this hole."@en) -AnnotationAssertion( "the smell of this portion of mozzarella"@en) -AnnotationAssertion( "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) -AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (role) - -AnnotationAssertion( "role") -AnnotationAssertion( "Role") -AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) -AnnotationAssertion( "the priest role"@en) -AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) -AnnotationAssertion( "the role of a building in serving as a military target"@en) -AnnotationAssertion( "the role of a stone in marking a property boundary"@en) -AnnotationAssertion( "the role of subject in a clinical trial"@en) -AnnotationAssertion( "the student role"@en) -AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) -AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) -AnnotationAssertion(rdfs:label "role"@en) -SubClassOf( ) - -# Class: (fiat object) - -AnnotationAssertion( "fiat-object") -AnnotationAssertion( "FiatObjectPart") -AnnotationAssertion( "or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29"@en) -AnnotationAssertion( "the FMA:regional parts of an intact human body."@en) -AnnotationAssertion( "the Western hemisphere of the Earth"@en) -AnnotationAssertion( "the division of the brain into regions"@en) -AnnotationAssertion( "the division of the planet into hemispheres"@en) -AnnotationAssertion( "the dorsal and ventral surfaces of the body"@en) -AnnotationAssertion( "the upper and lower lobes of the left lung"@en) -AnnotationAssertion( "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions"@en) -AnnotationAssertion(rdfs:label "fiat object"@en) -SubClassOf( ) - -# Class: (object aggregate) - -AnnotationAssertion( "object-aggregate") -AnnotationAssertion( "ObjectAggregate") -AnnotationAssertion( "a collection of cells in a blood biobank."@en) -AnnotationAssertion( "a swarm of bees is an aggregate of members who are linked together through natural bonds"@en) -AnnotationAssertion( "a symphony orchestra"@en) -AnnotationAssertion( "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)"@en) -AnnotationAssertion( "defined by fiat: the aggregate of members of an organization"@en) -AnnotationAssertion( "defined through physical attachment: the aggregate of atoms in a lump of granite"@en) -AnnotationAssertion( "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container"@en) -AnnotationAssertion( "defined via attributive delimitations such as: the patients in this hospital"@en) -AnnotationAssertion( "the aggregate of bearings in a constant velocity axle joint"@en) -AnnotationAssertion( "the aggregate of blood cells in your body"@en) -AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) -AnnotationAssertion( "the restaurants in Palo Alto"@en) -AnnotationAssertion( "your collection of Meissen ceramic plates."@en) -AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) -AnnotationAssertion(rdfs:label "object aggregate"@en) -SubClassOf( ) - -# Class: (site) - -AnnotationAssertion( "site") -AnnotationAssertion( "Site") -AnnotationAssertion( "Manhattan Canyon)"@en) -AnnotationAssertion( "a hole in the interior of a portion of cheese"@en) -AnnotationAssertion( "a rabbit hole"@en) -AnnotationAssertion( "an air traffic control region defined in the airspace above an airport"@en) -AnnotationAssertion( "the Grand Canyon"@en) -AnnotationAssertion( "the Piazza San Marco"@en) -AnnotationAssertion( "the cockpit of an aircraft"@en) -AnnotationAssertion( "the hold of a ship"@en) -AnnotationAssertion( "the interior of a kangaroo pouch"@en) -AnnotationAssertion( "the interior of the trunk of your car"@en) -AnnotationAssertion( "the interior of your bedroom"@en) -AnnotationAssertion( "the interior of your office"@en) -AnnotationAssertion( "the interior of your refrigerator"@en) -AnnotationAssertion( "the lumen of your gut"@en) -AnnotationAssertion( "your left nostril (a fiat part – the opening – of your left nasal cavity)"@en) -AnnotationAssertion(rdfs:label "site"@en) -SubClassOf( ) - -# Class: (object) - -AnnotationAssertion( "object") -AnnotationAssertion( "Object") -AnnotationAssertion( "atom"@en) -AnnotationAssertion( "cell"@en) -AnnotationAssertion( "cells and organisms"@en) -AnnotationAssertion( "engineered artifacts"@en) -AnnotationAssertion( "grain of sand"@en) -AnnotationAssertion( "molecule"@en) -AnnotationAssertion( "organelle"@en) -AnnotationAssertion( "organism"@en) -AnnotationAssertion( "planet"@en) -AnnotationAssertion( "solid portions of matter"@en) -AnnotationAssertion( "star"@en) -AnnotationAssertion( "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting."@en) -AnnotationAssertion( "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)."@en) -AnnotationAssertion( "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47"@en) -AnnotationAssertion( "BFO 2 Reference: an object is a maximal causally unified material entity"@en) -AnnotationAssertion( "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74"@en) -AnnotationAssertion(rdfs:label "object"@en) -SubClassOf( ) - -# Class: (generically dependent continuant) - -AnnotationAssertion( "gdc") -AnnotationAssertion( "GenericallyDependentContinuant") -AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) -AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) -AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) -AnnotationAssertion( "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) -AnnotationAssertion(rdfs:label "generically dependent continuant"@en) -SubClassOf( ) - -# Class: (function) - -AnnotationAssertion( "function") -AnnotationAssertion( "Function") -AnnotationAssertion( "the function of a hammer to drive in nails"@en) -AnnotationAssertion( "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en) -AnnotationAssertion( "the function of amylase in saliva to break down starch into sugar"@en) -AnnotationAssertion( "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc."@en) -AnnotationAssertion(rdfs:label "function"@en) -SubClassOf( ) - -# Class: (process boundary) - -AnnotationAssertion( "p-boundary") -AnnotationAssertion( "ProcessBoundary") -AnnotationAssertion( "the boundary between the 2nd and 3rd year of your life."@en) -AnnotationAssertion(rdfs:label "process boundary"@en) -SubClassOf( ) - -# Class: (one-dimensional temporal region) - -AnnotationAssertion( "1d-t-region") -AnnotationAssertion( "OneDimensionalTemporalRegion") -AnnotationAssertion( "the temporal region during which a process occurs."@en) -AnnotationAssertion( "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)."@en) -AnnotationAssertion(rdfs:label "one-dimensional temporal region"@en) -SubClassOf( ) - -# Class: (material entity) - -AnnotationAssertion( "material") -AnnotationAssertion( "MaterialEntity") -AnnotationAssertion( "a flame"@en) -AnnotationAssertion( "a forest fire"@en) -AnnotationAssertion( "a human being"@en) -AnnotationAssertion( "a hurricane"@en) -AnnotationAssertion( "a photon"@en) -AnnotationAssertion( "a puff of smoke"@en) -AnnotationAssertion( "a sea wave"@en) -AnnotationAssertion( "a tornado"@en) -AnnotationAssertion( "an aggregate of human beings."@en) -AnnotationAssertion( "an energy wave"@en) -AnnotationAssertion( "an epidemic"@en) -AnnotationAssertion( "the undetached arm of a human being"@en) -AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) -AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) -AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) -AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) -AnnotationAssertion(rdfs:label "material entity"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (continuant fiat boundary) - -AnnotationAssertion( "cf-boundary") -AnnotationAssertion( "ContinuantFiatBoundary") -AnnotationAssertion( "BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions."@en) -AnnotationAssertion( "BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29"@en) -AnnotationAssertion( "Every continuant fiat boundary is located at some spatial region at every time at which it exists"@en) -AnnotationAssertion(rdfs:label "continuant fiat boundary"@en) -SubClassOf( ) - -# Class: (immaterial entity) - -AnnotationAssertion( "immaterial") -AnnotationAssertion( "ImmaterialEntity") -AnnotationAssertion( "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10"@en) -AnnotationAssertion(rdfs:label "immaterial entity"@en) -SubClassOf( ) - -# Class: (process profile) - -AnnotationAssertion( "process-profile") -AnnotationAssertion( "ProcessProfile") -AnnotationAssertion( "On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels"@en) -AnnotationAssertion( "One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance."@en) -AnnotationAssertion( "The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on."@en) -AnnotationAssertion(rdfs:label "process profile"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (history) - -AnnotationAssertion( "history") -AnnotationAssertion( "History") -AnnotationAssertion(rdfs:label "history"@en) -SubClassOf( ) - -# Class: (immune response) - -AnnotationAssertion( "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immune response") -SubClassOf( ) - -# Class: (biological_process) - -AnnotationAssertion( "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "biological_process") -SubClassOf( ) - -# Class: (entry into host) - -AnnotationAssertion( "Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "entry into host") -SubClassOf( ) - -# Class: (establishment of localization) - -AnnotationAssertion( "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.") -AnnotationAssertion( ) -AnnotationAssertion( "Gene Ontology: http://purl.obolibrary.org/obo/go.owl") -AnnotationAssertion(rdfs:label "establishment of localization") -SubClassOf( ) - -# Class: (multi-organism process) - -AnnotationAssertion( "A biological process which involves another organism of the same or different species.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "multi-organism process") -SubClassOf( ) - -# Class: (data item) - -AnnotationAssertion(rdfs:label "data item"@en) -SubClassOf( ) - -# Class: (information content entity) - -AnnotationAssertion(rdfs:label "information content entity"@en) -SubClassOf( ) - -# Class: (curation status specification) - -AnnotationAssertion( "curation status specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) -AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) -AnnotationAssertion( "PERSON:Bill Bug"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion( "OBI_0000266"@en) -AnnotationAssertion(rdfs:label "curation status specification"@en) -EquivalentClasses( ObjectOneOf( )) -SubClassOf( ) - -# Class: (data about an ontology part) - -AnnotationAssertion( "data about an ontology part is a data item about a part of an ontology, for example a term"@en) -AnnotationAssertion( "Person:Alan Ruttenberg") -AnnotationAssertion(rdfs:label "data about an ontology part"@en) -SubClassOf( ) - -# Class: (obsolescence reason specification) - -AnnotationAssertion( "obsolescence reason specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) -AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) -EquivalentClasses( ObjectOneOf( )) -SubClassOf( ) - -# Class: (denotator type) - -AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities.") -AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective.") -AnnotationAssertion( "Alan Ruttenberg") -AnnotationAssertion( "Barry Smith, Werner Ceusters") -AnnotationAssertion(rdfs:label "denotator type") -EquivalentClasses( ObjectOneOf( )) -SubClassOf( ) - -# Class: (opportunistic infectious disposition) - -AnnotationAssertion( "An infectious disposition to become part of a disorder only in organisms whose defenses are compromised."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion( "opportunitistic pathogenic disposition"@en) -AnnotationAssertion(rdfs:comment "The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.") -AnnotationAssertion(rdfs:comment "This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin)."@en) -AnnotationAssertion(rdfs:label "opportunistic infectious disposition"@en) -SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectAllValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))))))) - -# Class: (primary infectious disposition) - -AnnotationAssertion( "An infectious disposition to become part of a disorder in organisms that have intact defenses."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.") -AnnotationAssertion(rdfs:comment "A quote from page 3 of Mandell's \"Principles and Practice of Infectious Diseases\" (Sixth edition): \"It is useful to distinguish \"principal\" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease.\"") -AnnotationAssertion(rdfs:label "primary infectious disposition"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))))) -SubClassOf( ) - -# Class: (pathogenic disposition) - -AnnotationAssertion( "A disposition to initiate processes that result in a disorder."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion( "pathogenicity"@en) -AnnotationAssertion(rdfs:comment "A pathogenic disposition is realized in processes that create a disorder.") -AnnotationAssertion(rdfs:comment "The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.") -AnnotationAssertion(rdfs:label "pathogenic disposition"@en) -SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectAllValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (infectious disposition) - -AnnotationAssertion( "A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder.") -AnnotationAssertion(rdfs:label "infectious disposition"@en) -SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectAllValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))) - -# Class: (zoonotic disposition) - -AnnotationAssertion( "An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis.") -AnnotationAssertion(rdfs:label "zoonotic disposition"@en) -SubClassOf( ) - -# Class: (reverse zoonotic disposition) - -AnnotationAssertion( "An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis.") -AnnotationAssertion(rdfs:label "reverse zoonotic disposition"@en) -SubClassOf( ) - -# Class: (immunocompetent organism) - -AnnotationAssertion( "An organism that has immunocompetence."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:label "immunocompetent organism"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (infectious agent transmissibility) - -AnnotationAssertion( "A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.") -AnnotationAssertion(rdfs:label "infectious agent transmissibility"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectivity) - -AnnotationAssertion( "A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "This quality is measured by the proportion of exposed who become infected.") -AnnotationAssertion(rdfs:label "infectivity"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (virulence) - -AnnotationAssertion( "A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal. "@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "This quality is measured by the proportion of clinically apparent cases that are severe or fatal.") -AnnotationAssertion(rdfs:label "virulence"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (susceptibility) - -AnnotationAssertion( "A quality that inheres in an entity and is the degree to which it can be harmed by another entity."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.") -AnnotationAssertion(rdfs:label "susceptibility"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectious disease incidence) - -AnnotationAssertion( "A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.") -AnnotationAssertion(rdfs:label "infectious disease incidence"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infection incidence) - -AnnotationAssertion( "A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.") -AnnotationAssertion(rdfs:label "infection incidence"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectious disease incidence proportion) - -AnnotationAssertion( "A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time. "@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion( "cumulative incidence of infectious disease"@en) -AnnotationAssertion(rdfs:comment "An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured.") -AnnotationAssertion(rdfs:label "infectious disease incidence proportion"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infection incidence proportion) - -AnnotationAssertion( "A quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time. "@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion( "cumulative incidence of infection"@en) -AnnotationAssertion(rdfs:comment "An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured.") -AnnotationAssertion(rdfs:label "infection incidence proportion"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectious disease incidence rate) - -AnnotationAssertion( "A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured.") -AnnotationAssertion(rdfs:label "infectious disease incidence rate"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infection incidence rate) - -AnnotationAssertion( "A quality that inheres in an organism population and is the infection incidence proportion per unit time."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured.") -AnnotationAssertion(rdfs:label "infection incidence rate"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectious disease prevalence) - -AnnotationAssertion( "A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.") -AnnotationAssertion(rdfs:label "infectious disease prevalence"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infection prevalence) - -AnnotationAssertion( "A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.") -AnnotationAssertion(rdfs:label "infection prevalence"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectious disease lifetime prevalence) - -AnnotationAssertion( "A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics.") -AnnotationAssertion(rdfs:label "infectious disease lifetime prevalence"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectious agent seroprevalence) - -AnnotationAssertion( "A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics.") -AnnotationAssertion(rdfs:label "infectious agent seroprevalence"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectious disease mortality rate) - -AnnotationAssertion( "A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year.") -AnnotationAssertion(rdfs:label "infectious disease mortality rate"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectious disease endemicity) - -AnnotationAssertion( "A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic.") -AnnotationAssertion(rdfs:label "infectious disease endemicity"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (infectious disease sporadicity) - -AnnotationAssertion( "A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "Sporadic quality of infectious disease is relational to previous prevalence of the disease.") -AnnotationAssertion(rdfs:label "infectious disease sporadicity"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (organism population) - -AnnotationAssertion( "An aggregate of organisms of the same Species."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.") -AnnotationAssertion(rdfs:label "organism population"@en) -SubClassOf( ) - -# Class: (pathogen) - -AnnotationAssertion( "A material entity with a pathogenic disposition."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:label "pathogen"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (primary pathogen) - -AnnotationAssertion( "An infectious agent with a primary infectious disposition."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion( "principal pathogen") -AnnotationAssertion(rdfs:label "primary pathogen"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (host) - -AnnotationAssertion( "An organism bearing a host role."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:label "host"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (infectious agent) - -AnnotationAssertion( "An organism that has an infectious disposition."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:label "infectious agent"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - -# Class: (immunosuppression) - -AnnotationAssertion( "A process that attenuates an immune response."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:label "immunosuppression"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (immunocompetence) - -AnnotationAssertion( "A disposition that is the ability to mount a normal immune response."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response.") -AnnotationAssertion(rdfs:label "immunocompetence"@en) -SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectAllValuesFrom( ))) -DisjointClasses( ) - -# Class: (communicability) - -AnnotationAssertion( "An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "The disposition is realized in a direct, horizontal transmission process between members of the same Species.") -AnnotationAssertion(rdfs:label "communicability"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))) -SubClassOf( ) - -# Class: (establishment of localization in host) - -AnnotationAssertion( "An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature."@en) -AnnotationAssertion( "Requested addition of this term to the GO.") -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:comment "An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA."@en) -AnnotationAssertion(rdfs:label "establishment of localization in host"@en) -EquivalentClasses( ObjectSomeValuesFrom( )) -SubClassOf( ) - -# Class: (appearance of disorder) - -AnnotationAssertion( "A process by which a disorder comes into existence."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:label "appearance of disorder"@en) -EquivalentClasses( ObjectSomeValuesFrom( )) -SubClassOf( ) - -# Class: (host role) - -AnnotationAssertion( "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism."@en) -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alexander Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:label "host role"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))) - -# Class: (opportunistic pathogen) - -AnnotationAssertion( "An infectious agent with an opportunistic infectious disposition.") -AnnotationAssertion( "Albert Goldfain") -AnnotationAssertion( "Alex Diehl") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion( "opportunist") -AnnotationAssertion(rdfs:label "opportunistic pathogen") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (horizontal pathogen transmission process) - -AnnotationAssertion( "A pathogen transmission process in which a pathogen is transmitted from one host to another of the same Species, and the two hosts are not in a parent-child relationship.") -AnnotationAssertion( "Lindsay Cowell") -AnnotationAssertion(rdfs:label "horizontal pathogen transmission process") -SubClassOf( ) - -# Class: (Viruses) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "Viruses") -SubClassOf( ) - -# Class: (Bacteria) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "Bacteria") -SubClassOf( ) - -# Class: (Archaea) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "Archaea") -SubClassOf( ) - -# Class: (Eukaryota) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "Eukaryota") -SubClassOf( ) - -# Class: (Homo sapiens) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "Homo sapiens") -SubClassOf( ) - -# Class: (organism) - -AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organism"@en) -EquivalentClasses( ObjectUnionOf( )) -SubClassOf( ) -DisjointClasses( ) - -# Class: (disease) - -AnnotationAssertion( "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "disease") -SubClassOf( ) - -# Class: (disorder) - -AnnotationAssertion( "A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "disorder") -SubClassOf( ) - -# Class: (disease course) - -AnnotationAssertion( "The totality of all processes through which a given disease instance is realized."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "disease course") -SubClassOf( ) - -# Class: (extended organism) - -AnnotationAssertion( "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "extended organism") -SubClassOf( ) - -# Class: (transmission process) - -AnnotationAssertion( "A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.") -AnnotationAssertion( "Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species.") -AnnotationAssertion( "Suggested label: pathogen transmission process") -AnnotationAssertion( ) -AnnotationAssertion( "Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl") -AnnotationAssertion(rdfs:label "transmission process") -SubClassOf( ) - -# Class: (Obsolete Class) - -AnnotationAssertion(rdfs:label "Obsolete Class") - -# Class: () - -EquivalentClasses( ObjectOneOf()) -SubClassOf( ) - - -############################ -# Named Individuals -############################ - -# Individual: (example to be eventually removed) - -AnnotationAssertion(rdfs:label "example to be eventually removed"@en) - -# Individual: (failed exploratory term) - -AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) -AnnotationAssertion( "Person:Alan Ruttenberg") -AnnotationAssertion(rdfs:label "failed exploratory term"@en) - -# Individual: (metadata complete) - -AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) -AnnotationAssertion(rdfs:label "metadata complete"@en) - -# Individual: (organizational term) - -AnnotationAssertion( "term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) -AnnotationAssertion(rdfs:label "organizational term"@en) - -# Individual: (ready for release) - -AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) -AnnotationAssertion(rdfs:label "ready for release"@en) - -# Individual: (metadata incomplete) - -AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) -AnnotationAssertion(rdfs:label "metadata incomplete"@en) - -# Individual: (uncurated) - -AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) -AnnotationAssertion(rdfs:label "uncurated"@en) - -# Individual: (pending final vetting) - -AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) -AnnotationAssertion(rdfs:label "pending final vetting"@en) - -# Individual: (core) - -AnnotationAssertion( "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion(rdfs:label "core"@en) - -# Individual: (placeholder removed) - -AnnotationAssertion(rdfs:label "placeholder removed"@en) - -# Individual: (terms merged) - -AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) -AnnotationAssertion(rdfs:label "terms merged"@en) - -# Individual: (term imported) - -AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) -AnnotationAssertion(rdfs:label "term imported"@en) - -# Individual: (term split) - -AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) -AnnotationAssertion(rdfs:label "term split"@en) - -# Individual: (universal) - -AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.") -AnnotationAssertion( "Alan Ruttenberg") -AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf") -AnnotationAssertion(rdfs:label "universal") - -# Individual: (defined class) - -AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal") -AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.") -AnnotationAssertion( "Alan Ruttenberg") -AnnotationAssertion(rdfs:label "defined class") - -# Individual: (named class expression) - -AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.") -AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions") -AnnotationAssertion( "Alan Ruttenberg") -AnnotationAssertion(rdfs:label "named class expression") - -# Individual: (to be replaced with external ontology term) - -AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) - -# Individual: (requires discussion) - -AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "requires discussion"@en) - - -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -AnnotationAssertion( " - -## 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 +# Class: obo:IDO_0000479 (infectious disease incidence) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000479 "A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000479 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000479 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000479 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000479 "A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.") +AnnotationAssertion(rdfs:label obo:IDO_0000479 "infectious disease incidence"@en) +SubClassOf(obo:IDO_0000479 obo:BFO_0000019) + +# Class: obo:IDO_0000480 (infection incidence) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000480 "A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000480 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000480 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000480 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000480 "A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.") +AnnotationAssertion(rdfs:label obo:IDO_0000480 "infection incidence"@en) +SubClassOf(obo:IDO_0000480 obo:BFO_0000019) + +# Class: obo:IDO_0000481 (infectious disease incidence proportion) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000481 "A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time. "@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000481 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000481 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000481 "Lindsay Cowell") +AnnotationAssertion(obo:IAO_0000118 obo:IDO_0000481 "cumulative incidence of infectious disease"@en) +AnnotationAssertion(rdfs:comment obo:IDO_0000481 "An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured.") +AnnotationAssertion(rdfs:label obo:IDO_0000481 "infectious disease incidence proportion"@en) +SubClassOf(obo:IDO_0000481 obo:BFO_0000019) + +# Class: obo:IDO_0000482 (infection incidence proportion) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000482 "A quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time. "@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000482 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000482 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000482 "Lindsay Cowell") +AnnotationAssertion(obo:IAO_0000118 obo:IDO_0000482 "cumulative incidence of infection"@en) +AnnotationAssertion(rdfs:comment obo:IDO_0000482 "An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured.") +AnnotationAssertion(rdfs:label obo:IDO_0000482 "infection incidence proportion"@en) +SubClassOf(obo:IDO_0000482 obo:BFO_0000019) + +# Class: obo:IDO_0000483 (infectious disease incidence rate) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000483 "A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000483 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000483 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000483 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000483 "An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured.") +AnnotationAssertion(rdfs:label obo:IDO_0000483 "infectious disease incidence rate"@en) +SubClassOf(obo:IDO_0000483 obo:BFO_0000019) + +# Class: obo:IDO_0000484 (infection incidence rate) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000484 "A quality that inheres in an organism population and is the infection incidence proportion per unit time."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000484 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000484 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000484 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000484 "An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured.") +AnnotationAssertion(rdfs:label obo:IDO_0000484 "infection incidence rate"@en) +SubClassOf(obo:IDO_0000484 obo:BFO_0000019) + +# Class: obo:IDO_0000485 (infectious disease prevalence) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000485 "A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000485 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000485 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000485 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000485 "Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.") +AnnotationAssertion(rdfs:label obo:IDO_0000485 "infectious disease prevalence"@en) +SubClassOf(obo:IDO_0000485 obo:BFO_0000019) + +# Class: obo:IDO_0000486 (infection prevalence) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000486 "A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000486 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000486 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000486 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000486 "Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.") +AnnotationAssertion(rdfs:label obo:IDO_0000486 "infection prevalence"@en) +SubClassOf(obo:IDO_0000486 obo:BFO_0000019) + +# Class: obo:IDO_0000487 (infectious disease lifetime prevalence) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000487 "A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000487 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000487 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000487 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000487 "Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics.") +AnnotationAssertion(rdfs:label obo:IDO_0000487 "infectious disease lifetime prevalence"@en) +SubClassOf(obo:IDO_0000487 obo:BFO_0000019) + +# Class: obo:IDO_0000488 (infectious agent seroprevalence) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000488 "A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000488 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000488 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000488 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000488 "Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics.") +AnnotationAssertion(rdfs:label obo:IDO_0000488 "infectious agent seroprevalence"@en) +SubClassOf(obo:IDO_0000488 obo:BFO_0000019) + +# Class: obo:IDO_0000489 (infectious disease mortality rate) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000489 "A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000489 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000489 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000489 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000489 "A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year.") +AnnotationAssertion(rdfs:label obo:IDO_0000489 "infectious disease mortality rate"@en) +SubClassOf(obo:IDO_0000489 obo:BFO_0000019) + +# Class: obo:IDO_0000623 (communicability) + +AnnotationAssertion(obo:IAO_0000115 obo:IDO_0000623 "An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000623 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000623 "Alexander Diehl") +AnnotationAssertion(obo:IAO_0000117 obo:IDO_0000623 "Lindsay Cowell") +AnnotationAssertion(rdfs:comment obo:IDO_0000623 "The disposition is realized in a direct, horizontal transmission process between members of the same Species.") +AnnotationAssertion(rdfs:label obo:IDO_0000623 "communicability"@en) -This interpretation is *not* the same as an at-all-times relation -") -AnnotationAssertion(rdfs:label "axiom holds for all times"@en) ) \ No newline at end of file diff --git a/src/ontology/imports/mf_import.owl b/src/ontology/imports/mf_import.owl index 2b7eca0..f59e1cd 100644 --- a/src/ontology/imports/mf_import.owl +++ b/src/ontology/imports/mf_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2026-03-13") +Annotation(owl:versionInfo "2026-07-19") Declaration(Class()) Declaration(Class()) @@ -88,6 +88,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -247,6 +248,23 @@ AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:label "curator note"@en) +# Annotation Property: (term tracker item) + +AnnotationAssertion( "term tracker item") +AnnotationAssertion( "term tracker item"@en) +AnnotationAssertion( "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/") +AnnotationAssertion( "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An IRI or similar locator for a request or discussion of an ontology term.") +AnnotationAssertion( "An IRI or similar locator for a request or discussion of an ontology term."@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg") +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg") +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term.") +AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) +AnnotationAssertion(rdfs:label "term tracker item"@en) + # Annotation Property: (imported from) AnnotationAssertion( "imported from"@en) @@ -322,24 +340,28 @@ AnnotationAssertion(rdfs:label "ter AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") AnnotationAssertion(rdfs:label "has broad synonym"@en) # Annotation Property: (has exact synonym) AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") AnnotationAssertion(rdfs:label "has exact synonym"@en) # Annotation Property: (has narrow synonym) AnnotationAssertion( "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") AnnotationAssertion(rdfs:label "has narrow synonym"@en) # Annotation Property: (has related synonym) AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") AnnotationAssertion(rdfs:label "has related synonym"@en) @@ -975,6 +997,7 @@ AnnotationAssertion(rdfs:label "req AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") AnnotationAssertion(rdfs:label "out of scope") diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl new file mode 100644 index 0000000..12c564b --- /dev/null +++ b/src/ontology/imports/obi_import.owl @@ -0,0 +1,647 @@ +Prefix(:=) +Prefix(dc:=) +Prefix(obo:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) +Prefix(terms:=) +Prefix(protege:=) +Prefix(oboInOwl:=) + + +Ontology( + +Annotation(dc:source ) +Annotation(owl:versionInfo "2026-07-19") + +Declaration(Class(obo:BFO_0000040)) +Declaration(Class(obo:COB_0001300)) +Declaration(Class(obo:IAO_0000005)) +Declaration(Class(obo:IAO_0000027)) +Declaration(Class(obo:IAO_0000030)) +Declaration(Class(obo:IAO_0000032)) +Declaration(Class(obo:IAO_0000033)) +Declaration(Class(obo:IAO_0000038)) +Declaration(Class(obo:IAO_0000104)) +Declaration(Class(obo:IAO_0000572)) +Declaration(Class(obo:IAO_0000577)) +Declaration(Class(obo:OBI_0000066)) +Declaration(Class(obo:OBI_0000115)) +Declaration(Class(obo:OBI_0000227)) +Declaration(Class(obo:OBI_0000245)) +Declaration(Class(obo:OBI_0000425)) +Declaration(Class(obo:OBI_0000471)) +Declaration(Class(obo:OBI_0000576)) +Declaration(Class(obo:OBI_0000658)) +Declaration(Class(obo:OBI_0000674)) +Declaration(Class(obo:OBI_0000679)) +Declaration(Class(obo:OBI_0000714)) +Declaration(Class(obo:OBI_0001092)) +Declaration(Class(obo:OBI_0001173)) +Declaration(Class(obo:OBI_0001226)) +Declaration(Class(obo:OBI_0001293)) +Declaration(Class(obo:OBI_0001454)) +Declaration(Class(obo:OBI_0001530)) +Declaration(Class(obo:OBI_0001554)) +Declaration(Class(obo:OBI_0001615)) +Declaration(Class(obo:OBI_0001628)) +Declaration(Class(obo:OBI_0001629)) +Declaration(Class(obo:OBI_0001931)) +Declaration(Class(obo:OBI_0001933)) +Declaration(Class(obo:OBI_0001958)) +Declaration(Class(obo:OBI_0002110)) +Declaration(Class(obo:OBI_0200000)) +Declaration(Class(obo:OBI_0200166)) +Declaration(Class(obo:OBI_0200170)) +Declaration(Class(obo:OBI_0300311)) +Declaration(Class(obo:OBI_0302867)) +Declaration(Class(obo:OBI_0302914)) +Declaration(Class(obo:OBI_0400107)) +Declaration(Class(obo:OBI_0500000)) +Declaration(Class(obo:OBI_0500020)) +Declaration(ObjectProperty(obo:BFO_0000051)) +Declaration(ObjectProperty(obo:OBI_0000293)) +Declaration(ObjectProperty(obo:OBI_0000299)) +Declaration(ObjectProperty(obo:OBI_0000308)) +Declaration(ObjectProperty(obo:OBI_0000312)) +Declaration(ObjectProperty(obo:OBI_0000417)) +Declaration(ObjectProperty(obo:OBI_0001938)) +Declaration(ObjectProperty(obo:RO_0000056)) +Declaration(ObjectProperty(obo:RO_0000057)) +Declaration(ObjectProperty(oboInOwl:ObsoleteProperty)) +Declaration(AnnotationProperty(obo:IAO_0000111)) +Declaration(AnnotationProperty(obo:IAO_0000112)) +Declaration(AnnotationProperty(obo:IAO_0000114)) +Declaration(AnnotationProperty(obo:IAO_0000115)) +Declaration(AnnotationProperty(obo:IAO_0000116)) +Declaration(AnnotationProperty(obo:IAO_0000117)) +Declaration(AnnotationProperty(obo:IAO_0000118)) +Declaration(AnnotationProperty(obo:IAO_0000119)) +Declaration(AnnotationProperty(obo:IAO_0000231)) +Declaration(AnnotationProperty(obo:IAO_0000232)) +Declaration(AnnotationProperty(obo:OBI_0001847)) +Declaration(AnnotationProperty(obo:OBI_0001886)) +Declaration(AnnotationProperty(dc:source)) +############################ +# Annotation Properties +############################ + +# Annotation Property: obo:OBI_0001847 (ISA alternative term) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001847 "ISA alternative term"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001847 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001847 "An alternative term used by the ISA tools project (http://isa-tools.org)."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0001847 "Requested by Alejandra Gonzalez-Beltran +https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001847 "Person: Alejandra Gonzalez-Beltran") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001847 "Person: Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001847 "ISA tools project (http://isa-tools.org)") +AnnotationAssertion(rdfs:label obo:OBI_0001847 "ISA alternative term"@en) +SubAnnotationPropertyOf(obo:OBI_0001847 obo:IAO_0000118) + +# Annotation Property: obo:OBI_0001886 (NIAID GSCID-BRC alternative term) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001886 "NIAID GSCID-BRC alternative term"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001886 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001886 "An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001886 "PERSON: Chris Stoeckert, Jie Zheng") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001886 "NIAID GSCID-BRC metadata working group") +AnnotationAssertion(rdfs:label obo:OBI_0001886 "NIAID GSCID-BRC alternative term"@en) +SubAnnotationPropertyOf(obo:OBI_0001886 obo:IAO_0000118) + + +############################ +# Object Properties +############################ + +# Object Property: obo:OBI_0000293 (has specified input) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000293 "has specified input") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000293 "see is_input_of example_of_usage"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000293 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000293 "The inverse property of is specified input of") +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000293 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Bjoern Peters") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Larry Hunter") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Melanie Coutot") +AnnotationAssertion(rdfs:label obo:OBI_0000293 "has specified input"@en) +SubObjectPropertyOf(obo:OBI_0000293 obo:RO_0000057) + +# Object Property: obo:OBI_0000299 (has specified output) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000299 "has specified output") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000299 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000299 "The inverse property of is specified output of") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Bjoern Peters") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Larry Hunter") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Melanie Courtot") +AnnotationAssertion(rdfs:label obo:OBI_0000299 "has specified output"@en) +SubObjectPropertyOf(obo:OBI_0000299 obo:RO_0000057) +InverseObjectProperties(obo:OBI_0000299 obo:OBI_0000312) + +# Object Property: obo:OBI_0000308 (obsolete_realizes) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000308 "realizes") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000308 "example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the +function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' +denotes a function and not a process). We leave open the possibility of defining +in future the sub-relations directly_realizes (as bewteen a function and it's +functioning) and indirectly_realizes.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000308 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000308 "Relation between a process and a function, where the unfolding of the +process requires the execution of the function. Class level: P realizes F iff: +given any p that instantiates P, there exists some f, t such that f instantiates + F at t and p *realizes* f. Here, *realizes* is the primitive +instance level relation [GOC:cjm]"@en) +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000308 "replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes'") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000308 "GROUP:OBI:") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000308 "PERSON: Chris Mungal") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000308 "executes") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000308 "has_function_part") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000308 "involves_execution_of") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000308 "is_realization_of") +AnnotationAssertion(obo:IAO_0000231 obo:OBI_0000308 obo:IAO_0000228) +AnnotationAssertion(rdfs:label obo:OBI_0000308 "obsolete_realizes"@en) +SubObjectPropertyOf(obo:OBI_0000308 oboInOwl:ObsoleteProperty) + +# Object Property: obo:OBI_0000312 (is specified output of) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000312 "is specified output of") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000312 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000312 "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000312 "Alan Ruttenberg"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000312 "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label obo:OBI_0000312 "is specified output of"@en) +SubObjectPropertyOf(obo:OBI_0000312 obo:RO_0000056) + +# Object Property: obo:OBI_0000417 (achieves_planned_objective) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000417 "achieves_planned_objective") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000417 "A cell sorting process achieves the objective specification 'material separation objective'") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000417 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000417 "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000417 "BP, AR, PPPB branch") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000417 "PPPB branch derived") +AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000417 "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch") +AnnotationAssertion(rdfs:label obo:OBI_0000417 "achieves_planned_objective") +ObjectPropertyRange(obo:OBI_0000417 obo:IAO_0000005) + +# Object Property: obo:OBI_0001938 (has value specification) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001938 "has value specification") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001938 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001938 "A relation between an information content entity and a value specification that specifies its value."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001938 "PERSON: James A. Overton") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001938 "OBI") +AnnotationAssertion(rdfs:label obo:OBI_0001938 "has value specification") +SubObjectPropertyOf(obo:OBI_0001938 obo:BFO_0000051) +ObjectPropertyDomain(obo:OBI_0001938 obo:IAO_0000030) +ObjectPropertyRange(obo:OBI_0001938 obo:OBI_0001933) + + + +############################ +# Classes +############################ + +# Class: obo:OBI_0000066 (investigation) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000066 "investigation"@en) +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000066 "Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000066 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000066 "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000066 "Bjoern Peters"@en) +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000066 "OBI branch derived"@en) +AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000066 "Could add specific objective specification"@en) +AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000066 "Following OBI call November 2012,26th: it was decided there was no need for adding achieves objective of drawing conclusion as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS"@en) +AnnotationAssertion(obo:OBI_0001847 obo:OBI_0000066 "study") +AnnotationAssertion(rdfs:label obo:OBI_0000066 "investigation"@en) +SubClassOf(obo:OBI_0000066 ObjectSomeValuesFrom(obo:BFO_0000051 obo:IAO_0000572)) +SubClassOf(obo:OBI_0000066 ObjectSomeValuesFrom(obo:BFO_0000051 obo:OBI_0000471)) + +# Class: obo:OBI_0000115 (intervention design) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000115 "intervention design") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000115 "PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000115 obo:IAO_0000125) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000115 "An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000115 "Philppe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000115 "OBI branch derived") +AnnotationAssertion(rdfs:label obo:OBI_0000115 "intervention design") +SubClassOf(obo:OBI_0000115 obo:OBI_0500000) + +# Class: obo:OBI_0000227 (data encoding) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000227 "data encoding"@en) +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000227 "storage of measurement results from an assay into a text file, such as"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000227 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000227 "a documenting process to encode an information entity into a digital document"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000227 "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000227 "OBI branch derived"@en) +AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000227 "We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE"@en) +AnnotationAssertion(rdfs:label obo:OBI_0000227 "data encoding"@en) +SubClassOf(obo:OBI_0000227 obo:IAO_0000572) + +# Class: obo:OBI_0000245 (organization) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000245 "organization"@en) +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000245 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods."@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000245 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000245 "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000245 "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers + +2) there are organization_roles (employer, owner, vendor, patent holder) + +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. + +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. + +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. + +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Alan Ruttenberg") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Bjoern Peters") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000245 "PERSON: Susanna Sansone") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000245 "GROUP: OBI") +AnnotationAssertion(rdfs:label obo:OBI_0000245 "organization"@en) +SubClassOf(obo:OBI_0000245 obo:BFO_0000040) + +# Class: obo:OBI_0000425 (averaging objective) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000425 "averaging objective"@en) +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000425 "A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment."@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000425 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000425 "An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000425 "Elisabetta Manduchi") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000425 "James Malone"@en) +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000425 "PERSON: Elisabetta Manduchi") +AnnotationAssertion(rdfs:label obo:OBI_0000425 "averaging objective"@en) +SubClassOf(obo:OBI_0000425 obo:OBI_0200166) + +# Class: obo:OBI_0000471 (study design execution) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000471 "study design execution") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000471 "injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000471 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000471 "a planned process that carries out a study design"@en) +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000471 "removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000471 "branch derived") +AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000471 "6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.") +AnnotationAssertion(rdfs:label obo:OBI_0000471 "study design execution") + +# Class: obo:OBI_0000576 (scattered molecular aggregate) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000576 "scattered molecular aggregate") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000576 "the sodium and chloride ions in a glass of salt water") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000576 obo:IAO_0000123) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000576 "a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000576 "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000576 "Collective"@en) +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000576 "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349"@en) +AnnotationAssertion(rdfs:label obo:OBI_0000576 "scattered molecular aggregate"@en) +SubClassOf(obo:OBI_0000576 obo:BFO_0000040) + +# Class: obo:OBI_0000658 (data representational model) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000658 "data representational model") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000658 "The Cytoscape application is commonly used to visualize data representational models about biological entities. It can read and write several serializations of data representational models, including BioPAX."@en) +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000658 "gene regulatory graph model") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000658 "phylogenetic tree") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000658 "protein interaction network") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000658 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000658 "An information content entity representing the relationships between data items."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000658 "Melanie Courtot") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000658 "data structure") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000658 "data structure specification") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000658 "GROUP: OBI") +AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000658 "2009-02-28: work on this term has been finalized during the OBI workshop winter 2009") +AnnotationAssertion(rdfs:label obo:OBI_0000658 "data representational model") +SubClassOf(obo:OBI_0000658 obo:IAO_0000033) + +# Class: obo:OBI_0000674 (center value) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000674 "center value") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000674 obo:IAO_0000125) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000674 "A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000674 "PERSON: James Malone") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000674 "PERSON: Monnie McGee") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000674 "median") +AnnotationAssertion(rdfs:label obo:OBI_0000674 "center value"@en) +SubClassOf(obo:OBI_0000674 obo:IAO_0000027) + +# Class: obo:OBI_0000679 (average value) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000679 "average value") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000679 obo:IAO_0000125) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000679 "A data item that is produced as the output of an averaging data transformation and represents the average value of the input data."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000679 "PERSON: James Malone") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000679 "PERSON: Monnie McGee") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0000679 "arithmetic mean") +AnnotationAssertion(rdfs:label obo:OBI_0000679 "average value"@en) +SubClassOf(obo:OBI_0000679 obo:IAO_0000027) + +# Class: obo:OBI_0000714 (graph of vertices) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000714 "graph of vertices") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000714 "For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000714 obo:IAO_0000123) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000714 "A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000714 "Bjoern Peters") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000714 "Chris Stoeckert") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000714 "James Malone") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000714 "WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html") +AnnotationAssertion(rdfs:label obo:OBI_0000714 "graph of vertices") +SubClassOf(obo:OBI_0000714 obo:IAO_0000038) + +# Class: obo:OBI_0001092 (computer cluster) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001092 "computer cluster") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001092 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001092 "A group of linked computers, working together closely so that in many respects they form a single computer."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001092 "PERSON: Erik Segerdell") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001092 "http://en.wikipedia.org/wiki/Cluster_(computing)") +AnnotationAssertion(rdfs:label obo:OBI_0001092 "computer cluster") +SubClassOf(obo:OBI_0001092 obo:OBI_0400107) + +# Class: obo:OBI_0001173 (service) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001173 "service") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001173 "providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001173 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001173 "A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001173 "Carlo; Matt") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001173 "OBI workshop San Diego 2011") +AnnotationAssertion(rdfs:label obo:OBI_0001173 "service") + +# Class: obo:OBI_0001226 (environmental history design) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001226 "environmental history design") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001226 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001226 "A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001226 "Person: Chris Stoeckert, Jie Zheng") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001226 "MO_698 environmental_history_design") +AnnotationAssertion(rdfs:label obo:OBI_0001226 "environmental history design") +SubClassOf(obo:OBI_0001226 obo:OBI_0500000) + +# Class: obo:OBI_0001293 (disease state design) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001293 "disease state design") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001293 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001293 "A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001293 "Person: Chris Stoeckert, Jie Zheng") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001293 "MO_902 disease_state_design") +AnnotationAssertion(rdfs:label obo:OBI_0001293 "disease state design") +SubClassOf(obo:OBI_0001293 obo:OBI_0500000) + +# Class: obo:OBI_0001454 (pathogenicity design) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001454 "pathogenicity design") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001454 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001454 "A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001454 "Person: Chris Stoeckert, Jie Zheng") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001454 "MO_807 pathogenicity_design") +AnnotationAssertion(rdfs:label obo:OBI_0001454 "pathogenicity design") +SubClassOf(obo:OBI_0001454 obo:OBI_0500000) + +# Class: obo:OBI_0001530 (data service) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001530 "data service") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001530 "Data analysis service such statistical abalysis or storage service such data backup.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001530 obo:IAO_0000125) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001530 "A service that has some information content entity as input and output."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001530 "PERSON: Carlo Torniai") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001530 "PERSON: Matthew Brush") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001530 "PERSON: Carlo Torniai") +AnnotationAssertion(rdfs:comment obo:OBI_0001530 "Information content entity was used as specified input and output since it was more appropriate then data item or dataset.") +AnnotationAssertion(rdfs:label obo:OBI_0001530 "data service") +SubClassOf(obo:OBI_0001530 obo:OBI_0001173) +SubClassOf(obo:OBI_0001530 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000030)) +SubClassOf(obo:OBI_0001530 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000030)) + +# Class: obo:OBI_0001554 (rate measurement datum) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001554 "rate measurement datum") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001554 "The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001554 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001554 "A scalar measurement datum that represents the number of events occuring over a time interval"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001554 "PERSON: Bjoern Peters, Randi Vita") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001554 "IEDB") +AnnotationAssertion(rdfs:label obo:OBI_0001554 "rate measurement datum") +SubClassOf(obo:OBI_0001554 obo:IAO_0000032) + +# Class: obo:OBI_0001615 (investigation description) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001615 "investigation description"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001615 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001615 "A textual entity that describes an investigation."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001615 "Person: Chris Stoeckert, Jie Zheng"@en) +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001615 "NIAID GSCID-BRC metadata working group"@en) +AnnotationAssertion(obo:OBI_0001847 obo:OBI_0001615 "study description") +AnnotationAssertion(obo:OBI_0001886 obo:OBI_0001615 "project description"@en) +AnnotationAssertion(dc:source obo:OBI_0001615 "NIAID GSCID-BRC") +AnnotationAssertion(rdfs:label obo:OBI_0001615 "investigation description"@en) + +# Class: obo:OBI_0001628 (investigation identifier) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001628 "investigation identifier"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001628 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001628 "A CRID symbol used to identify an investigation."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001628 "Person: Chris Stoeckert, Jie Zhneg"@en) +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001628 "NIAID GSCID-BRC metadata working group"@en) +AnnotationAssertion(obo:OBI_0001886 obo:OBI_0001628 "project ID"@en) +AnnotationAssertion(dc:source obo:OBI_0001628 "NIAID GSCID-BRC") +AnnotationAssertion(rdfs:label obo:OBI_0001628 "investigation identifier"@en) +SubClassOf(obo:OBI_0001628 obo:IAO_0000577) + +# Class: obo:OBI_0001629 (grant identifier) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001629 "grant identifier"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001629 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001629 "A CRID symbol used to identify a grant."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001629 "Person: Chris Stoeckert, Jie Zheng"@en) +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0001629 "NIAID GSCID-BRC metadata working group"@en) +AnnotationAssertion(obo:OBI_0001886 obo:OBI_0001629 "grant ID"@en) +AnnotationAssertion(dc:source obo:OBI_0001629 "NIAID GSCID-BRC") +AnnotationAssertion(rdfs:label obo:OBI_0001629 "grant identifier"@en) +SubClassOf(obo:OBI_0001629 obo:IAO_0000577) + +# Class: obo:OBI_0001931 (scalar value specification) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001931 "scalar value specification") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001931 obo:IAO_0000123) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001931 "A value specification that consists of two parts: a numeral and a unit label"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001931 "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label obo:OBI_0001931 "scalar value specification") +SubClassOf(obo:OBI_0001931 obo:OBI_0001933) + +# Class: obo:OBI_0001933 (value specification) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001933 "value specification") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001933 "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001933 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001933 "An information content entity that specifies a value within a classification scheme or on a quantitative scale."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0001933 "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001933 "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label obo:OBI_0001933 "value specification") +SubClassOf(obo:OBI_0001933 obo:IAO_0000030) + +# Class: obo:OBI_0001958 (systematic review study design) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0001958 "systematic review study design") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001958 "Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0001958 "The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0001958 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0001958 "A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0001958 "PERSON: Bill Hogan") +AnnotationAssertion(rdfs:label obo:OBI_0001958 "systematic review study design") +SubClassOf(obo:OBI_0001958 obo:OBI_0500000) + +# Class: obo:OBI_0002110 (digital object identifier) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0002110 "digital object identifier"@en) +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0002110 "The doi symbol: \"10.1109/5.771073\" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0002110 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0002110 "A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0002110 "Discussed on Aug 22, 2016 OBI dev call. Details see tracker: +https://sourceforge.net/p/obi/obi-terms/818/") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0002110 "OBI developers") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0002110 "DOI") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0002110 "https://en.wikipedia.org/wiki/Digital_object_identifier +https://www.doi.org/") +AnnotationAssertion(rdfs:label obo:OBI_0002110 "digital object identifier"@en) +SubClassOf(obo:OBI_0002110 obo:IAO_0000577) + +# Class: obo:OBI_0200000 (data transformation) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0200000 "data transformation"@en) +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0200000 "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0200000 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200000 "A completely executed planned process that produces output data from input data."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Elisabetta Manduchi"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Helen Parkinson"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "James Malone"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Melanie Courtot"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Richard Scheuermann"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Ryan Brinkman"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200000 "Tina Hernandez-Boussard"@en) +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0200000 "data analysis"@en) +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0200000 "data processing"@en) +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0200000 "Branch editors"@en) +AnnotationAssertion(rdfs:label obo:OBI_0200000 "data transformation"@en) +SubClassOf(obo:OBI_0200000 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000027) ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000027))) +SubClassOf(obo:OBI_0200000 ObjectAllValuesFrom(obo:OBI_0000293 obo:IAO_0000027)) + +# Class: obo:OBI_0200166 (data transformation objective) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0200166 "data transformation objective"@en) +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0200166 "normalize objective"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0200166 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200166 "An objective specification to transformation input data into output data"@en) +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0200166 "Modified definition in 2013 Philly OBI workshop") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200166 "James Malone"@en) +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0200166 "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label obo:OBI_0200166 "data transformation objective"@en) +SubClassOf(obo:OBI_0200166 obo:IAO_0000005) + +# Class: obo:OBI_0200170 (averaging data transformation) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0200170 "averaging data transformation"@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0200170 obo:IAO_0000123) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200170 "An averaging data transformation is a data transformation that has objective averaging."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0200170 "James Malone") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0200170 "PERSON: James Malone"@en) +AnnotationAssertion(rdfs:label obo:OBI_0200170 "averaging data transformation"@en) +SubClassOf(obo:OBI_0200170 obo:OBI_0200000) + +# Class: obo:OBI_0300311 (observation design) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0300311 "observation design") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0300311 "PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0300311 obo:IAO_0000125) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0300311 "observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0300311 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0300311 "OBI branch derived") +AnnotationAssertion(rdfs:label obo:OBI_0300311 "observation design") +SubClassOf(obo:OBI_0300311 obo:OBI_0500000) + +# Class: obo:OBI_0302867 (predicted data item) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0302867 "predicted data item") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0302867 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0302867 "A data item that was generated on the basis of a calculation or logical reasoning"@en) +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0302867 "BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted.") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0302867 "Philippe Rocca-Serra; Bjoern Peters") +AnnotationAssertion(rdfs:label obo:OBI_0302867 "predicted data item"@en) +SubClassOf(obo:OBI_0302867 obo:IAO_0000027) + +# Class: obo:OBI_0302914 (digital curation) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0302914 "digital curation") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0302914 "PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44."@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0302914 obo:IAO_0000120) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0302914 "Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0302914 "Philippe Rocca-Serra") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0302914 "wikipedia") +AnnotationAssertion(rdfs:label obo:OBI_0302914 "digital curation"@en) +SubClassOf(obo:OBI_0302914 obo:IAO_0000572) + +# Class: obo:OBI_0400107 (computer) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0400107 "computer") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0400107 "Apple PowerBook, Dell OptiPlex") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0400107 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0400107 "A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0400107 "Melanie Courtot") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0400107 "Trish Whetzel") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0400107 "http://en.wikipedia.org/wiki/Computer") +AnnotationAssertion(rdfs:label obo:OBI_0400107 "computer") +SubClassOf(obo:OBI_0400107 obo:COB_0001300) + +# Class: obo:OBI_0500000 (study design) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0500000 "study design"@en) +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0500000 "a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design."@en) +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0500000 obo:IAO_0000122) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0500000 "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OBI_0500000 "Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.") +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0500000 "PERSON: Chris Stoeckert") +AnnotationAssertion(obo:IAO_0000118 obo:OBI_0500000 "experimental design"@en) +AnnotationAssertion(obo:IAO_0000232 obo:OBI_0500000 "rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol."@en) +AnnotationAssertion(rdfs:label obo:OBI_0500000 "study design"@en) +SubClassOf(obo:OBI_0500000 obo:IAO_0000104) + +# Class: obo:OBI_0500020 (time series design) + +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0500020 "time series design") +AnnotationAssertion(obo:IAO_0000112 obo:OBI_0500020 "PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.") +AnnotationAssertion(obo:IAO_0000114 obo:OBI_0500020 obo:IAO_0000125) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0500020 "Groups of assays that are related as part of a time series."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OBI_0500020 "Philippe Rocca-Serra on behalf of MO") +AnnotationAssertion(obo:IAO_0000119 obo:OBI_0500020 "MO_887") +AnnotationAssertion(rdfs:label obo:OBI_0500020 "time series design") +SubClassOf(obo:OBI_0500020 obo:OBI_0500000) + + +) \ No newline at end of file diff --git a/src/ontology/imports/obi_terms.txt b/src/ontology/imports/obi_terms.txt new file mode 100644 index 0000000..99e5043 --- /dev/null +++ b/src/ontology/imports/obi_terms.txt @@ -0,0 +1,38 @@ +COB_0000082 +COB_0000026 +COB_0000022 +COB_0001300 +OBI_0000115 +OBI_0000066 +OBI_0000227 +OBI_0000245 +OBI_0000425 +OBI_0000471 +OBI_0000576 +OBI_0000658 +OBI_0000674 +OBI_0000679 +OBI_0000714 +OBI_0001092 +OBI_0001173 +OBI_0001226 +OBI_0001293 +OBI_0001454 +OBI_0001530 +OBI_0001554 +OBI_0001615 +OBI_0001628 +OBI_0001629 +OBI_0001931 +OBI_0001933 +OBI_0001958 +OBI_0002110 +OBI_0200000 +OBI_0200166 +OBI_0200170 +OBI_0300311 +OBI_0302867 +OBI_0302914 +OBI_0400107 +OBI_0500000 +OBI_0500020 diff --git a/src/ontology/imports/ogms_import.owl b/src/ontology/imports/ogms_import.owl index 6eb1c4d..107fe45 100644 --- a/src/ontology/imports/ogms_import.owl +++ b/src/ontology/imports/ogms_import.owl @@ -13,15 +13,14 @@ Prefix(oboInOwl:=) Ontology( - + Annotation(dc:source ) -Annotation(owl:versionInfo "2026-03-13") +Annotation(owl:versionInfo "2026-07-19") Declaration(Class(obo:BFO_0000015)) Declaration(Class(obo:BFO_0000016)) Declaration(Class(obo:BFO_0000019)) Declaration(Class(obo:BFO_0000040)) -Declaration(Class(obo:OBI_0000011)) Declaration(Class(obo:OGMS_0000014)) Declaration(Class(obo:OGMS_0000018)) Declaration(Class(obo:OGMS_0000023)) @@ -29,6 +28,7 @@ Declaration(Class(obo:OGMS_0000027)) Declaration(Class(obo:OGMS_0000031)) Declaration(Class(obo:OGMS_0000032)) Declaration(Class(obo:OGMS_0000045)) +Declaration(Class(obo:OGMS_0000060)) Declaration(Class(obo:OGMS_0000063)) Declaration(Class(obo:OGMS_0000087)) Declaration(Class(obo:OGMS_0000090)) @@ -114,6 +114,13 @@ AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000045 "creation date: 2009-06-23T AnnotationAssertion(rdfs:label obo:OGMS_0000045 "disorder") SubClassOf(obo:OGMS_0000045 obo:BFO_0000040) +# Class: obo:OGMS_0000060 (bodily process) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000060 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000060 "creation date: 2009-06-23T11:53:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000060 "bodily process") +SubClassOf(obo:OGMS_0000060 obo:BFO_0000015) + # Class: obo:OGMS_0000063 (disease course) AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000063 "The totality of all processes through which a given disease instance is realized."@en) @@ -163,7 +170,6 @@ AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000096 "http://groups.google.com/g AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000096 "creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18") AnnotationAssertion(rdfs:label obo:OGMS_0000096 "health care process") -SubClassOf(obo:OGMS_0000096 obo:OBI_0000011) # Class: obo:OGMS_0000097 (health care encounter) diff --git a/src/ontology/imports/omrse_import.owl b/src/ontology/imports/omrse_import.owl index 338b251..7e38e32 100644 --- a/src/ontology/imports/omrse_import.owl +++ b/src/ontology/imports/omrse_import.owl @@ -7,10 +7,11 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2026-03-13") + +Annotation( ) +Annotation(owl:versionInfo "2026-07-19") +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -64,7 +65,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -270,6 +270,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -283,6 +284,8 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -295,6 +298,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) +Declaration(Datatype(xsd:date)) ############################ # Annotation Properties ############################ @@ -353,26 +357,6 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) -AnnotationAssertion( "2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:label "definition") @@ -388,7 +372,7 @@ AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:label "editor note"@en) -# Annotation Property: (term editor) +# Annotation Property: (definition editor) AnnotationAssertion( "term editor"@en) AnnotationAssertion( ) @@ -400,7 +384,7 @@ AnnotationAssertion(rdfs:label "def AnnotationAssertion(rdfs:label "definition editor"@en) AnnotationAssertion(rdfs:label "term editor"@en) -# Annotation Property: (alternative term) +# Annotation Property: (alternative label) AnnotationAssertion( "alternative label"@en) AnnotationAssertion( ) @@ -438,6 +422,19 @@ AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:label "curator note"@en) +# Annotation Property: (term tracker item) + +AnnotationAssertion( "term tracker item"@en) +AnnotationAssertion( "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) +AnnotationAssertion( "the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A URL for a request or discussion of an ontology term."@en) +AnnotationAssertion( "An IRI or similar locator for a request or discussion of an ontology term."@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) +AnnotationAssertion(rdfs:label "term tracker item"@en) + # Annotation Property: (imported from) AnnotationAssertion( "imported from"@en) @@ -510,20 +507,25 @@ AnnotationAssertion(rdfs:label "ter AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") AnnotationAssertion(rdfs:label "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") -# Annotation Property: (has cross-reference) +# Annotation Property: (database_cross_reference) AnnotationAssertion( "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string") AnnotationAssertion( "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.") +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( "2024-03-18"^^xsd:date) +AnnotationAssertion(rdfs:label "database_cross_reference") AnnotationAssertion(rdfs:label "has cross-reference") # Annotation Property: (has exact synonym) AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") AnnotationAssertion(rdfs:label "has exact synonym"@en) AnnotationAssertion(rdfs:label "has_exact_synonym") @@ -531,15 +533,22 @@ AnnotationAssertion(rdfs:label "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") AnnotationAssertion(rdfs:label "has narrow synonym"@en) # Annotation Property: (has_related_synonym) AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") AnnotationAssertion(rdfs:label "has related synonym"@en) AnnotationAssertion(rdfs:label "has_related_synonym") +# Annotation Property: rdfs:label (label) + +AnnotationAssertion(rdfs:label rdfs:label "label") +AnnotationAssertion(rdfs:label rdfs:label "label"@en) + ############################ # Object Properties @@ -756,7 +765,7 @@ SubObjectPropertyOf( owl:topObjec ObjectPropertyDomain( ObjectSomeValuesFrom( )) ObjectPropertyRange( ) -# Object Property: (inheres in) +# Object Property: (characteristic of) AnnotationAssertion( "inheres in"@en) AnnotationAssertion( "this fragility is a characteristic of this vase"@en) @@ -769,7 +778,7 @@ SubObjectPropertyOf( ) FunctionalObjectProperty() -# Object Property: (bearer of) +# Object Property: (has characteristic) AnnotationAssertion( "bearer of"@en) AnnotationAssertion( "this apple is bearer of this red color"@en) @@ -1207,6 +1216,7 @@ SubObjectPropertyOf( (causally upstream of, positive effect) AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "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 "causally upstream of, positive effect") SubObjectPropertyOf( ) @@ -1215,6 +1225,7 @@ SubObjectPropertyOf( (causally upstream of, negative effect) AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causally upstream of, negative effect") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1900,6 +1911,13 @@ ObjectPropertyDomain( (educational facility) + +AnnotationAssertion( "Published") +AnnotationAssertion( "A facility in which formal education is provided to a student population.") +AnnotationAssertion(rdfs:label "educational facility") +SubClassOf( ) + # Class: (count) AnnotationAssertion( "A measurement datum that is the output of counting."@en) @@ -1915,7 +1933,7 @@ AnnotationAssertion( "William R. Hogan") AnnotationAssertion( "A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification."@en) AnnotationAssertion(rdfs:label "geographical movement of organism"@en) -SubClassOf( ) +SubClassOf( ) # Class: (human travel) @@ -2229,6 +2247,7 @@ SubClassOf( (biological_process) AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24968"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Biological_process") AnnotationAssertion( "biological process") AnnotationAssertion( "physiological process") @@ -2287,11 +2306,11 @@ AnnotationAssertion( "action specification"@en) SubClassOf( ) -# Class: (data item) +# Class: (data entity) -AnnotationAssertion( "data item"@en) +AnnotationAssertion( "data entity"@en) AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) -AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion( "An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) @@ -2307,7 +2326,8 @@ AnnotationAssertion( "PERSON: Chris Stoeckert"@en) AnnotationAssertion( "PERSON: Jonathan Rees"@en) AnnotationAssertion( "data"@en) -AnnotationAssertion(rdfs:label "data item"@en) +AnnotationAssertion( "data item"@en) +AnnotationAssertion(rdfs:label "data entity"@en) SubClassOf( ) # Class: (information content entity) @@ -2349,18 +2369,18 @@ AnnotationAssertion(rdfs:label "cur EquivalentClasses( ObjectOneOf( )) SubClassOf( ) -# Class: (data set) +# Class: (homogenous data collection) -AnnotationAssertion( "data set"@en) +AnnotationAssertion( "homogenous data collection"@en) AnnotationAssertion( "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en) AnnotationAssertion( "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en) AnnotationAssertion( "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type"@en) AnnotationAssertion( "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.") AnnotationAssertion( "person:Allyson Lister"@en) AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000042"@en) +AnnotationAssertion( "data set"@en) AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "data set"@en) +AnnotationAssertion(rdfs:label "homogenous data collection"@en) SubClassOf( ) # Class: (data about an ontology part) @@ -2781,11 +2801,12 @@ SubClassOf( ObjectSomeValuesFrom( # Class: (school facility) -AnnotationAssertion( "A facility that is run by a school organization and is the bearer of a school function."@en) +AnnotationAssertion( "An educational facility that is run by a school organization and is the bearer of a school function."@en) AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "school facility"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (secondary school role) @@ -3018,6 +3039,7 @@ AnnotationAssertion(rdfs:label "req AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype."@en) AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "out of scope") @@ -3092,27 +3114,28 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( 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( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( 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( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +AnnotationAssertion(rdfs:label "William R. Hogan"@en) ) \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index a806e5e..5ba5b79 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2026-03-13") +Annotation(owl:versionInfo "2026-07-19") Declaration(Class()) Declaration(Class()) @@ -25,6 +25,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -194,6 +197,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -214,6 +218,8 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -229,6 +235,7 @@ Declaration(AnnotationProperty( Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) +Declaration(Datatype(xsd:date)) ############################ # Annotation Properties ############################ @@ -338,6 +345,17 @@ AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:label "curator note"@en) +# Annotation Property: (term tracker item) + +AnnotationAssertion( "term tracker item"@en) +AnnotationAssertion( "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An IRI or similar locator for a request or discussion of an ontology term."@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) +AnnotationAssertion(rdfs:label "term tracker item"@en) + # Annotation Property: (imported from) AnnotationAssertion( "imported from"@en) @@ -444,6 +462,7 @@ SubAnnotationPropertyOf( AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") AnnotationAssertion(rdfs:label "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") @@ -451,7 +470,9 @@ AnnotationAssertion(rdfs:label "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string") AnnotationAssertion( "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.") +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( "2024-03-18"^^xsd:date) AnnotationAssertion(rdfs:label "database_cross_reference") AnnotationAssertion(rdfs:label "has cross-reference") @@ -459,6 +480,7 @@ AnnotationAssertion(rdfs:label "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") AnnotationAssertion(rdfs:label "has exact synonym"@en) AnnotationAssertion(rdfs:label "has_exact_synonym") @@ -466,6 +488,7 @@ AnnotationAssertion(rdfs:label "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") AnnotationAssertion(rdfs:label "has narrow synonym"@en) AnnotationAssertion(rdfs:label "has_narrow_synonym") @@ -473,6 +496,7 @@ AnnotationAssertion(rdfs:label "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") AnnotationAssertion(rdfs:label "has related synonym"@en) AnnotationAssertion(rdfs:label "has_related_synonym") @@ -1199,6 +1223,7 @@ SubObjectPropertyOf( (causally upstream of, positive effect) AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "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") @@ -1209,6 +1234,7 @@ SubObjectPropertyOf( (causally upstream of, negative effect) AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causally upstream of, negative effect") @@ -2098,6 +2124,27 @@ AnnotationAssertion(rdfs:label "imm SubClassOf( ) DisjointClasses( ObjectSomeValuesFrom( )) +# Class: (organism) + +AnnotationAssertion( "A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome"@en) +AnnotationAssertion( "'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'."@en) +AnnotationAssertion( "Includes virus - we will later have a class for cellular organisms."@en) +AnnotationAssertion(rdfs:label "organism"@en) +SubClassOf( ) + +# Class: (processed material entity) + +AnnotationAssertion( "A material entity processed by human activity with an intent to produce it."@en) +AnnotationAssertion( "In the COB 2024 workshop there was much disagreement about this label."@en) +AnnotationAssertion(rdfs:label "processed material entity"@en) +SubClassOf( ) + +# Class: (device) + +AnnotationAssertion( "A processed material entity which is designed to be capable of a process."@en) +AnnotationAssertion(rdfs:label "device"@en) +SubClassOf( ) + # Class: (molecular_function) AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index 54790e7..a318230 100644 --- a/src/ontology/imports/uberon_import.owl +++ b/src/ontology/imports/uberon_import.owl @@ -16,13 +16,13 @@ Prefix(foaf:=) Prefix(pato:=) Prefix(rdfs:=) Prefix(swrl:=) -Prefix(chebi:=) +Prefix(chebi:=) Prefix(sssom:=) Prefix(swrlb:=) Prefix(terms:=) -Prefix(chebi1:=) -Prefix(chebi2:=) -Prefix(chebi3:=) +Prefix(chebi1:=) +Prefix(chebi2:=) +Prefix(chebi3:=) Prefix(ubprop:=) Prefix(subsets:=) Prefix(oboInOwl:=) @@ -30,10 +30,12 @@ Prefix(ncbitaxon:=) Ontology( - -Annotation(dc:source ) -Annotation(owl:versionInfo "2026-03-13") + +Annotation(dc:source ) +Annotation(owl:versionInfo "2026-07-19") +Declaration(Class(obo:BFO_0000001)) +Declaration(Class(obo:BFO_0000015)) Declaration(Class(obo:BFO_0000040)) Declaration(Class(obo:UBERON_0000061)) Declaration(Class(obo:UBERON_0000071)) @@ -160,8 +162,6 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:UBERON_0000071 "XtroDO:0000085") AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:UBERON_0000071 "death") AnnotationAssertion(oboInOwl:id obo:UBERON_0000071 "UBERON:0000071") AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0000071 core:common_anatomy) -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0000071 core:human_subset) -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0000071 core:mouse_subset) AnnotationAssertion(rdfs:label obo:UBERON_0000071 "death stage") SubClassOf(obo:UBERON_0000071 obo:UBERON_0000105) @@ -185,10 +185,9 @@ AnnotationAssertion(oboInOwl:hasNarrowSynonym obo:UBERON_0000105 "stage") AnnotationAssertion(oboInOwl:id obo:UBERON_0000105 "UBERON:0000105") AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0000105 core:common_anatomy) AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0000105 core:efo_slim) -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0000105 core:human_subset) -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0000105 core:mouse_subset) AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0000105 core:upper_level) AnnotationAssertion(rdfs:label obo:UBERON_0000105 "life cycle stage") +SubClassOf(obo:UBERON_0000105 obo:BFO_0000015) # Class: obo:UBERON_0000465 (material anatomical entity) @@ -360,10 +359,9 @@ SubClassOf(obo:UBERON_0010000 obo:UBERON_0000061) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-6601-2165") obo:IAO_0000115 obo:UBERON_0035943 "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.") AnnotationAssertion(oboInOwl:id obo:UBERON_0035943 "UBERON:0035943") AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0035943 core:common_anatomy) -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0035943 core:human_subset) -AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0035943 core:mouse_subset) AnnotationAssertion(oboInOwl:inSubset obo:UBERON_0035943 core:upper_level) AnnotationAssertion(rdfs:label obo:UBERON_0035943 "life cycle temporal boundary") +SubClassOf(obo:UBERON_0035943 obo:BFO_0000001) ) \ No newline at end of file diff --git a/src/templates/external_import.tsv b/src/templates/external_import.tsv index 72711e7..d2e9317 100644 --- a/src/templates/external_import.tsv +++ b/src/templates/external_import.tsv @@ -2,3 +2,8 @@ ID Entity Type ID TYPE owl:Thing owl:Class http://humanbehaviourchange.org/ontology/BCIO_036000 owl:Class +http://purl.obolibrary.org/obo/COB_0000082 owl:Class +http://purl.obolibrary.org/obo/COB_0000026 owl:Class +http://purl.obolibrary.org/obo/COB_0000022 owl:Class +http://purl.obolibrary.org/obo/COB_0001300 owl:Class +